R vs Excel: inconsistent results after filtering

Question

this is my first post so please let me know if it doesn't meet standards or if anything is hard to follow. Thanks!

Given a data.table (or data.frame) of differential gene expression results (from CuffDiff), I want to filter these results by a q-value cutoff of <= 0.05 and fold change of >= 2 or fold change <= 0.5, producing 2 tables (one up, one down regulated genes). I am splitting these results after filtering by sample1_sample2 comparisons using data.table split() function, which seems to be doing fine, but lets imagine we're just talking about one up and one down list to keep things simple:

The problem is that I am getting inconsistent gene list lengths when I apply the same filters to the unfiltered data in Excel using the filter tool from the Data tab.. but ONLY for the up-regulated gene list! (fold change >= 2)

In RI tried filtering by data.table first, then another try with the filter() function from tidyverse. Same results as compared to the Excel filter.

Steps in R: -using data.table

# calculate fold change
cuffdat[, fold_change := 2^`log2(fold_change)`]
# filter by q <= 0.05
cuff_filt <- cuffdat[q_value <= 0.05]
# filter by fold change and separate into up and down-regulated lists
cuff_filt_up <- cuff_filt[fold_change >= 2]
cuff_filt_down <- cuff_filt[fold_change <= 0.5]

-using tidyverse

cuff_filt_tidy_up <- cuffdat %>% filter(q_value <= 0.05) %>% filter(fold_change >= 2)
cuff_filt_tidy_down <- cuffdat %>% filter(q_value <= 0.05) %>% filter(fold_change <= 0.5)

The results are written to an excel file with write.xlsx() from the openxlsx package.

Then I see that about 5 out of 10 lists of up-regulated (fold_change >= 2) genes have a different number of rows between R and Excel, usually 10 or under, BUT all of the Down regulated lists are consistent.

Am I making some mistake with the >= 2 fold change filter that's right under my nose and I can't see it? I made sure the number columns were of numeric type in both R and Excel attempts, still same results. Also made sure I was using greater-than-equal for both R and Excel, and the same q-value cutoff (<= 0.05).

Any help would be greatly appreciated, thank you for your time!

Pavlos

dput of data.table filtered for q <= 0.05 and fold_change >= 2 that is inconsistent with Excel results:

structure(list(gene = c("ABLIM3", "ACVRL1", "ADAMDEC1", "ADAP2", 
"ADM", "AIF1L", "ANXA3", "ARHGEF10L", "ASGR1", "ATP5EP2", "AZU1", 
"BAMBI", "BEX1", "BPI", "BST1", "C11orf45", "C1QA", "C1orf228", 
"C1orf54", "CALB1", "CALD1", "CCL13", "CCL2", "CCL3", "CCL5", 
"CCL7", "CCL8", "CD163", "CD180", "CD300E", "CD93", "CDC42EP1", 
"CEACAM4", "CEACAM6", "CELA2A", "CELA2B", "CFP", "CLDN10", "CLEC1B", 
"CLEC4A", "CLEC5A", "CLEC7A", "COL15A1", "COL17A1", "COL23A1", 
"CRTAM", "CSTA", "CTSG", "CTSH", "CXCL1", "CXCL10", "CXCL3", 
"CXCL8", "CYP27A1", "CYYR1", "DEFA3", "DEFA4", "DFNA5", "ECSCR", 
"ELANE", "EMP1", "FAM26E", "FCER2", "FCGR1B", "FCGR3A", "FCN1", 
"FGD2", "FGF22", "FGFR1", "FLT1", "FOLR3", "FPR3", "GALNT14", 
"GGTA1P", "GLT1D1", "GLT8D2", "GPBAR1", "GPNMB", "GPR37", "HBE1", 
"HBG1", "HGF", "HIST2H2AA4", "HIST2H3A", "HIST2H4A", "HNMT", 
"HTRA1", "HTRA4", "IGFBP2", "IGFBP5", "IGFL2", "IL6", "IL7R", 
"IRAK2", "IRF8", "IRG1", "KCNJ16", "KCNMB1", "KRT79", "LAMP3", 
"LGMN", "LILRB1", "LILRB4", "LINC00211", "LINC00599", "LINC01272", 
"LINC01554", "LOC101929076", "LOC101929371", "LRP3", "LYZ", "MARCKS", 
"MARCO", "MATN2", "MCEMP1", "MEFV", "METTL7B", "MGAM", "MPEG1", 
"MPO", "MS4A4A", "MS4A6A", "MS4A7", "MSR1", "MYOM1", "NAT8B", 
"NME8", "NNMT", "NRG1", "NRP1", "NXF3", "OLR1", "PALD1", "PCOLCE2", 
"PDE4B", "PID1", "PLA2G7", "PPARG", "PPBP", "PRTN3", "PTCRA", 
"PTGIR", "PTGR1", "PTPRB", "PTPRO", "RAB39A", "RASSF4", "REN", 
"RETN", "RGS13", "RND1", "RPS16", "RPS17", "S100A12", "S100A8", 
"S100A9", "S100P", "S100Z", "S1PR3", "SCGB3A1", "SEC14L5", "SEPT10", 
"SERPINA1", "SERPINE1", "SGK1", "SHROOM4", "SIGLEC1", "SIGLEC9", 
"SLAMF1", "SLAMF7", "SLAMF8", "SLC2A5", "SLC35F3", "SLC7A7", 
"SLPI", "SMIM24", "SNORD116-14", "SOWAHC", "SPARC", "SPR", "STEAP4", 
"STOX2", "SULT1C2", "TACSTD2", "TDRD6", "THBS4", "TLR8", "TMEM158", 
"TMEM40", "TMEM45B", "TMEM52B", "TNF", "TNNT1", "TREM1", "TREML1", 
"TRIM40", "UGT3A2", "VCAN", "VSTM1", "ZG16B"), sample_1 = c("Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
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"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
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"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
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"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", "Day7_WT", 
"Day7_WT"), sample_2 = c("Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", "Day7_P385L", 
"Day7_P385L", "Day7_P385L"), value_1 = c(0.196317, 1.09146, 20.8197, 
0.621022, 0.873852, 0.239717, 21.2973, 0.552663, 0.410193, 0, 
196.848, 0.396366, 68.9018, 41.2329, 16.7361, 0.214353, 3.55599, 
8.74624, 1.08134, 0.399986, 0.6367, 0.706357, 28.1959, 1.55592, 
3.797, 1.94343, 0.578803, 1.22134, 0.604323, 0.35601, 0.878815, 
0.110819, 6.49893, 18.7182, 0.144987, 0.0716135, 2.6455, 0.603466, 
1.78848, 2.11726, 5.30953, 5.84686, 0.150989, 0.555573, 1.15995, 
0.199626, 47.6079, 271.548, 11.9672, 0.291714, 2.93827, 0.836771, 
4.63867, 0.237466, 0.284529, 17.7825, 10.9124, 0.522299, 0.562429, 
782.655, 7.06801, 0.156979, 0.664455, 1.8181, 0.260624, 5.50522, 
0.931271, 0, 0.290243, 0.310714, 1.3432, 0.790291, 1.84662, 1.16774, 
0.271535, 0.113489, 0.321571, 2.98619, 0.163897, 9.42726, 101.271, 
10.029, 6.65174, 4.08239, 1.58604, 0.899613, 0.192766, 1.28342, 
17.5503, 1.15971, 0.262154, 0.71209, 2.85253, 0.831977, 3.14351, 
0.0991417, 0.13456, 0.115604, 0.242635, 0.366147, 1.03823, 0.1519, 
2.49728, 0.221398, 0.317481, 0.471214, 0.1555, 0.0780108, 0.949722, 
3.39944, 2383.57, 5.08801, 0.0907437, 0.814164, 7.79311, 0.692013, 
0.602081, 0.195118, 0.510745, 728.918, 0.39708, 3.32267, 2.21729, 
0.447134, 0.366244, 0.204145, 0.354241, 0.143136, 0.227235, 1.48332, 
2.33952, 0.18941, 0.518775, 0.935541, 1.33145, 0.707636, 1.95249, 
1.07082, 42.1945, 381.344, 0.204003, 0.952851, 2.58545, 0.114845, 
0.580007, 0.451847, 3.82407, 0.0717851, 10.5769, 0.276201, 0.250173, 
296.959, 1.83607, 1.59106, 197.05, 283.342, 28.1712, 0.648204, 
0.974485, 2.43853, 0.130732, 0.24136, 1.63849, 1.72731, 4.37642, 
0.184318, 0.122259, 0.852032, 0.397234, 0.621078, 1.13032, 7.06435, 
0.265075, 1.03216, 13.7835, 5.59732, 0, 0.250413, 5.37537, 1.13913, 
0.447285, 0.547311, 0.21776, 0.302822, 0.111735, 2.2128, 1.46586, 
0.147455, 0.514018, 0.323362, 0.191044, 0.655298, 0.675996, 3.88774, 
0.388337, 0.218507, 0.146101, 6.62815, 3.739, 1.20073), value_2 = c(0.45324, 
2.50031, 43.1896, 1.37394, 1.92193, 0.587226, 45.5257, 1.14778, 
0.830821, 0.959745, 623.059, 1.02135, 143.798, 117.852, 37.1248, 
0.673406, 10.062, 18.3545, 2.20377, 1.43024, 1.49143, 1.6134, 
108.017, 3.33157, 7.692, 5.63897, 2.15207, 2.69161, 2.77923, 
1.14163, 2.34804, 0.381354, 15.8248, 67.7769, 1.08107, 0.987541, 
6.02725, 1.69545, 4.26655, 5.72015, 16.2719, 16.485, 0.452521, 
2.28894, 2.65065, 0.535928, 108.571, 552.764, 39.5988, 0.944952, 
6.8774, 2.0748, 10.0979, 0.580245, 0.796667, 172.562, 124.344, 
1.13476, 1.30508, 2721.9, 15.2263, 0.394521, 1.61213, 3.66241, 
0.726946, 11.4552, 2.19551, 0.505434, 0.635273, 0.752423, 3.65331, 
1.83181, 4.50106, 2.88836, 0.7528, 0.295539, 0.750386, 7.07191, 
0.398168, 22.0268, 222.866, 21.1652, 19.6471, 11.6842, 4.972, 
3.10357, 0.492323, 2.68307, 41.6834, 4.42447, 0.924586, 1.71136, 
7.25159, 1.6908, 6.5702, 0.326422, 0.278229, 0.559898, 0.653446, 
0.734408, 2.11568, 0.3392, 5.12233, 0.479956, 0.875594, 1.05421, 
0.418637, 0.280914, 2.69293, 7.35105, 5011.98, 11.1341, 0.316893, 
1.89383, 17.2269, 1.50445, 1.4986, 0.459178, 1.3315, 1958.92, 
0.927596, 9.36493, 5.71188, 0.940312, 0.737134, 0.720338, 0.738963, 
0.513854, 0.458352, 3.61355, 4.96238, 0.467575, 1.10506, 4.05077, 
2.90378, 1.8309, 5.81191, 2.28018, 102.355, 1126.06, 0.554947, 
1.97704, 5.32462, 0.325342, 1.31397, 1.40889, 9.03869, 0.452779, 
29.6162, 0.664511, 0.560313, 616.394, 15.1201, 4.84659, 459.573, 
663.471, 56.7901, 1.38745, 2.06871, 6.59829, 0.297108, 0.520698, 
4.1477, 3.57958, 10.2514, 0.509629, 0.285103, 1.73761, 1.01281, 
1.59825, 2.36676, 20.8266, 0.644454, 2.42696, 41.5507, 15.5206, 
133.307, 0.700605, 11.4562, 2.2809, 1.42092, 1.23192, 0.993941, 
1.13313, 0.295785, 4.61433, 3.02764, 0.384398, 1.13122, 0.861308, 
0.703129, 1.34023, 1.94952, 8.3316, 0.798568, 0.490072, 0.377865, 
14.4932, 10.4012, 3.06693), `log2(fold_change)` = c(1.20709, 
1.19585, 1.05273, 1.1456, 1.1371, 1.29258, 1.09601, 1.05437, 
1.01824, Inf, 1.66229, 1.36557, 1.06143, 1.51511, 1.14941, 1.65149, 
1.5006, 1.0694, 1.02716, 1.83824, 1.22801, 1.19163, 1.93771, 
1.09844, 1.0185, 1.53683, 1.89458, 1.14, 2.20129, 1.6811, 1.41782, 
1.78293, 1.28391, 1.85635, 2.89847, 3.78554, 1.18796, 1.49032, 
1.25434, 1.43386, 1.61573, 1.49542, 1.58354, 2.04263, 1.19228, 
1.42474, 1.18936, 1.02546, 1.72637, 1.69569, 1.2269, 1.31007, 
1.12227, 1.28894, 1.4854, 3.27858, 3.51029, 1.11944, 1.21439, 
1.79816, 1.10719, 1.32953, 1.27872, 1.01036, 1.47988, 1.05713, 
1.23729, Inf, 1.13012, 1.27596, 1.44353, 1.21281, 1.28538, 1.30653, 
1.47113, 1.3808, 1.22249, 1.24379, 1.28059, 1.22435, 1.13796, 
1.07752, 1.50991, 1.51708, 1.6484, 1.78655, 1.35275, 1.0639, 
1.24798, 1.93174, 1.81839, 1.26501, 1.34606, 1.02309, 1.06356, 
1.71917, 1.04803, 2.27598, 1.42928, 1.00416, 1.02699, 1.15901, 
1.03645, 1.11626, 1.46359, 1.16171, 1.42878, 1.84838, 1.5036, 
1.11266, 1.07226, 1.12981, 1.80413, 1.21792, 1.14439, 1.12036, 
1.31558, 1.23471, 1.38238, 1.42623, 1.22407, 1.49493, 1.36517, 
1.07243, 1.00912, 1.81908, 1.06077, 1.84397, 1.01227, 1.28459, 
1.08482, 1.30368, 1.09095, 2.11432, 1.12493, 1.37148, 1.5737, 
1.09043, 1.27845, 1.56212, 1.44376, 1.05302, 1.04226, 1.50228, 
1.17979, 1.64066, 1.241, 2.65705, 1.48547, 1.26657, 1.1633, 1.05359, 
2.85003, 1.60698, 1.22173, 1.22749, 1.01142, 1.09792, 1.08602, 
1.43608, 1.18438, 1.10926, 1.33995, 1.05127, 1.228, 1.46725, 
1.22155, 1.02812, 1.3503, 1.36365, 1.06618, 1.5598, 1.28167, 
1.23348, 1.59193, 1.47138, Inf, 1.48429, 1.0917, 1.00167, 1.66756, 
1.17047, 2.19042, 1.90378, 1.40447, 1.06025, 1.04644, 1.38233, 
1.13799, 1.41338, 1.87989, 1.03225, 1.52803, 1.09966, 1.04011, 
1.16532, 1.37091, 1.12869, 1.47603, 1.35288), test_stat = c(2.00658, 
3.12429, 2.424, 2.43753, 2.28625, 2.28247, 3.58784, 2.39823, 
1.54227, NaN, 5.61646, 2.27268, 3.52845, 5.13617, 3.68527, 2.86682, 
3.69143, 3.25166, 1.36873, 3.55905, 2.94807, 1.77855, 6.02128, 
2.02959, 2.62256, 3.12736, 3.19038, 3.00659, 4.87099, 3.41242, 
3.93737, 2.1148, 3.58978, 6.25633, 2.98712, 2.89908, 3.03393, 
2.75607, 2.5763, 3.25455, 5.15589, 2.97127, 2.89412, 5.17953, 
2.98921, 1.98099, 3.77133, 3.46914, 5.39893, 2.25766, 2.85099, 
2.36709, 3.18018, 2.0055, 2.72056, 8.9142, 9.7305, 2.15298, 1.55361, 
5.57314, 3.52214, 1.85323, 2.34815, 2.43331, 2.27055, 2.89937, 
2.92172, NaN, 2.33767, 2.02357, 2.69521, 2.69065, 3.41086, 2.76604, 
2.55088, 1.5522, 1.91425, 3.57149, 2.10078, 3.33414, 3.6941, 
3.16165, 3.58832, 2.74836, 2.09147, 2.33757, 1.92201, 2.49338, 
4.02273, 5.55087, 1.85676, 2.14516, 4.13423, 2.44174, 3.00543, 
1.95182, 1.54677, 2.08118, 2.17697, 1.96473, 2.25559, 1.48895, 
1.91592, 1.60909, 2.71248, 2.11492, 1.8125, 1.93759, 2.44829, 
3.36387, 2.69839, 3.6309, 1.89572, 3.00854, 3.20829, 2.56388, 
1.70861, 2.5025, 2.8625, 3.72582, 1.95305, 3.98376, 3.74537, 
2.14768, 2.24282, 1.7964, 1.82806, 2.20893, 1.2864, 3.44472, 
2.79631, 1.52063, 2.48732, 4.798, 2.96266, 2.99639, 3.50158, 
2.37866, 4.27389, 5.1125, 1.23164, 2.28288, 2.26708, 2.98269, 
2.71301, 2.97294, 1.60518, 2.52803, 3.64556, 1.76986, 1.62913, 
3.14814, 4.61991, 2.47169, 4.08856, 4.12746, 2.91727, 1.81595, 
2.52568, 2.47716, 2.12052, 1.89482, 3.60961, 2.83426, 3.65856, 
3.07015, 2.10828, 2.06137, 2.4479, 2.90173, 2.59276, 4.71028, 
2.2375, 2.82056, 4.37469, 3.80344, NaN, 2.97173, 3.47577, 2.07544, 
3.81824, 2.74719, 3.79967, 3.20849, 1.51488, 2.93369, 2.86607, 
1.72571, 2.08725, 2.40333, 2.53293, 1.91473, 2.6328, 2.95305, 
1.49653, 1.68442, 1.75777, 3.76893, 3.60025, 2.42658), p_value = c(0.00095, 
5e-05, 5e-05, 5e-05, 3e-04, 5e-05, 5e-05, 5e-05, 0.00735, 5e-05, 
5e-05, 0.00035, 5e-05, 5e-05, 5e-05, 5e-05, 5e-05, 5e-05, 0.0153, 
5e-05, 5e-05, 0.00335, 5e-05, 0.0012, 5e-05, 5e-05, 5e-05, 5e-05, 
5e-05, 5e-05, 5e-05, 0.00275, 5e-05, 5e-05, 0.0011, 0.0081, 5e-05, 
5e-05, 5e-05, 5e-05, 5e-05, 5e-05, 5e-05, 5e-05, 5e-05, 0.0012, 
5e-05, 5e-05, 5e-05, 6e-04, 5e-05, 0.00045, 5e-05, 0.002, 5e-05, 
5e-05, 5e-05, 0.00055, 0.00895, 5e-05, 5e-05, 0.00615, 0.00015, 
5e-05, 2e-04, 5e-05, 5e-05, 5e-05, 1e-04, 2e-04, 5e-05, 5e-05, 
5e-05, 5e-05, 5e-05, 0.0134, 0.00135, 5e-05, 0.00095, 5e-05, 
5e-05, 5e-05, 5e-05, 5e-05, 0.00115, 0.00015, 0.00215, 5e-05, 
5e-05, 5e-05, 0.0047, 9e-04, 5e-05, 5e-05, 5e-05, 0.0036, 0.00215, 
0.00225, 5e-04, 0.00095, 0.00015, 0.0056, 6e-04, 0.0068, 1e-04, 
4e-04, 0.00435, 0.0047, 3e-04, 5e-05, 5e-05, 5e-05, 0.0058, 5e-05, 
5e-05, 1e-04, 0.00685, 1e-04, 5e-05, 5e-05, 0.00135, 5e-05, 5e-05, 
3e-04, 1e-04, 0.00695, 0.00275, 0.00185, 0.00475, 5e-05, 5e-05, 
0.0078, 0.00015, 5e-05, 5e-05, 5e-05, 5e-05, 1e-04, 5e-05, 5e-05, 
0.01345, 5e-05, 5e-05, 5e-05, 5e-05, 5e-05, 0.007, 0.0029, 5e-05, 
0.0052, 0.0071, 5e-05, 0.00025, 1e-04, 5e-05, 5e-05, 5e-05, 0.00265, 
5e-05, 5e-05, 5e-04, 0.0016, 5e-05, 5e-05, 5e-05, 5e-05, 0.0011, 
0.00065, 2e-04, 5e-05, 5e-05, 5e-05, 0.00045, 5e-05, 5e-05, 5e-05, 
0.01215, 5e-05, 5e-05, 2e-04, 5e-05, 5e-05, 5e-05, 5e-05, 0.01275, 
5e-05, 5e-05, 0.00775, 5e-04, 1e-04, 2e-04, 0.0017, 5e-05, 5e-05, 
0.0105, 0.0051, 0.0022, 5e-05, 5e-05, 1e-04), q_value = c(0.0042003, 
0.000285792, 0.000285792, 0.000285792, 0.00149098, 0.000285792, 
0.000285792, 0.000285792, 0.0253213, 0.000285792, 0.000285792, 
0.00171472, 0.000285792, 0.000285792, 0.000285792, 0.000285792, 
0.000285792, 0.000285792, 0.0475363, 0.000285792, 0.000285792, 
0.0127844, 0.000285792, 0.00516979, 0.000285792, 0.000285792, 
0.000285792, 0.000285792, 0.000285792, 0.000285792, 0.000285792, 
0.0107526, 0.000285792, 0.000285792, 0.00478529, 0.0275369, 0.000285792, 
0.000285792, 0.000285792, 0.000285792, 0.000285792, 0.000285792, 
0.000285792, 0.000285792, 0.000285792, 0.00516979, 0.000285792, 
0.000285792, 0.000285792, 0.00278595, 0.000285792, 0.00215195, 
0.000285792, 0.00812306, 0.000285792, 0.000285792, 0.000285792, 
0.0025768, 0.0300158, 0.000285792, 0.000285792, 0.021703, 0.000792744, 
0.000285792, 0.00103153, 0.000285792, 0.000285792, 0.000285792, 
0.000545769, 0.00103153, 0.000285792, 0.000285792, 0.000285792, 
0.000285792, 0.000285792, 0.0424478, 0.00573932, 0.000285792, 
0.0042003, 0.000285792, 0.000285792, 0.000285792, 0.000285792, 
0.000285792, 0.00497806, 0.000792744, 0.00865833, 0.000285792, 
0.000285792, 0.000285792, 0.0171816, 0.00400226, 0.000285792, 
0.000285792, 0.000285792, 0.0136142, 0.00865833, 0.0090128, 0.00236561, 
0.0042003, 0.000792744, 0.0200045, 0.00278595, 0.0236748, 0.000545769, 
0.00193503, 0.0160615, 0.0171816, 0.00149098, 0.000285792, 0.000285792, 
0.000285792, 0.020627, 0.000285792, 0.000285792, 0.000545769, 
0.023826, 0.000545769, 0.000285792, 0.000285792, 0.00573932, 
0.000285792, 0.000285792, 0.00149098, 0.000545769, 0.0241239, 
0.0107526, 0.00758166, 0.0173405, 0.000285792, 0.000285792, 0.0266545, 
0.000792744, 0.000285792, 0.000285792, 0.000285792, 0.000285792, 
0.000545769, 0.000285792, 0.000285792, 0.0425826, 0.000285792, 
0.000285792, 0.000285792, 0.000285792, 0.000285792, 0.0242703, 
0.0112665, 0.000285792, 0.0187596, 0.0245698, 0.000285792, 0.00126356, 
0.000545769, 0.000285792, 0.000285792, 0.000285792, 0.0104107, 
0.000285792, 0.000285792, 0.00236561, 0.006668, 0.000285792, 
0.000285792, 0.000285792, 0.000285792, 0.00478529, 0.00299287, 
0.00103153, 0.000285792, 0.000285792, 0.000285792, 0.00215195, 
0.000285792, 0.000285792, 0.000285792, 0.0390354, 0.000285792, 
0.000285792, 0.00103153, 0.000285792, 0.000285792, 0.000285792, 
0.000285792, 0.0406769, 0.000285792, 0.000285792, 0.0265047, 
0.00236561, 0.000545769, 0.00103153, 0.00703736, 0.000285792, 
0.000285792, 0.034456, 0.0184481, 0.00883654, 0.000285792, 0.000285792, 
0.000545769), fold_change = c(2.30871485566876, 2.29079760459197, 
2.07445160372441, 2.21238121881941, 2.19938474307908, 2.44965741127896, 
2.13762679927055, 2.07681110102276, 2.02544653048882, Inf, 3.16518538320374, 
2.57678112841665, 2.08699913132124, 2.85820619850681, 2.2182315976387, 
3.14157930616448, 2.82960367915901, 2.09856041899164, 2.03800840306513, 
3.57573544257798, 2.34243659891459, 2.284106626408, 3.83097072178747, 
2.14123033989948, 2.02581158584617, 2.90156248984729, 3.71813718202978, 
2.20381023175322, 4.5989037372092, 3.20672358303539, 2.6718147830246, 
3.44124354821656, 2.4349801306227, 3.62090418181883, 7.45635216305727, 
13.7898991415732, 2.27830358558026, 2.80951285226128, 2.38557988812945, 
2.70168598310707, 3.06466631524195, 2.81946219777292, 2.99704345072917, 
4.11995905591424, 2.28513595261415, 2.68466113698341, 2.28051553824233, 
2.03560832978275, 3.30894199097148, 3.23931776930728, 2.34063503686857, 
2.47953570478214, 2.17689225003702, 2.44348457956698, 2.79994793398733, 
9.70400302375208, 11.3946918121503, 2.17262622949865, 2.32042649909708, 
3.47776391533374, 2.15425644489321, 2.51320786487872, 2.42623618794283, 
2.0144137000668, 2.78925531931653, 2.08078802260224, 2.357552665982, 
Inf, 2.18876945167508, 2.42159902598884, 2.7198554881876, 2.3178866227572, 
2.43746246049362, 2.47345902466331, 2.77238957766824, 2.60412734540823, 
2.33349115688014, 2.36819848149628, 2.42938307848435, 2.33650155928769, 
2.2006962016317, 2.11040516418897, 2.84792272298791, 2.86211174482046, 
3.13485779445302, 3.44988913391344, 2.55398490818306, 2.09057528775145, 
2.37508640622967, 3.81515058040535, 3.5268739134304, 2.40328875732423, 
2.5421691022536, 2.03226706144957, 2.09008265983796, 3.29246932644883, 
2.06770446875457, 4.84326519342455, 2.69312277236306, 2.00577530706733, 
2.03776826845119, 2.23304140217502, 2.05117417052333, 2.16784258332078, 
2.75793795293665, 2.23722444638262, 2.69218956885596, 3.60095607144083, 
2.83549379655089, 2.16243984462348, 2.10272473343799, 2.18829918899484, 
3.49218502812462, 2.32611109253172, 2.21052645470794, 2.17401214511345, 
2.48902375616379, 2.35334037562828, 2.60698087645056, 2.68743525857218, 
2.33604813223885, 2.81850475226273, 2.57606679201964, 2.1029725226493, 
2.01268305030316, 3.52856112033918, 2.08604459528505, 3.58996555065788, 
2.01708237090597, 2.43612810488093, 2.12111082266887, 2.46857760502335, 
2.13014258039134, 4.32985886502834, 2.18090964436733, 2.58735856232568, 
2.9766714645419, 2.12937493753454, 2.42578216096095, 2.95287441434017, 
2.72028913259084, 2.07486863671876, 2.05945128416722, 2.83290063586317, 
2.26543798738013, 3.11808444475856, 2.36362309386873, 6.30741998718128, 
2.80008379160436, 2.40588886203887, 2.23969145963501, 2.07568856660972, 
7.2101536302576, 3.0461352507126, 2.3322622164661, 2.34159245132597, 
2.01589430621481, 2.14045870132923, 2.12287584700376, 2.70584650193043, 
2.27265705936133, 2.15734962216724, 2.53142545389945, 2.07235333121472, 
2.34242036243762, 2.76494349974408, 2.3319712464418, 2.03936498855291, 
2.5496513846185, 2.57335411926508, 2.09388179393958, 2.94812970869304, 
2.43120239300172, 2.35133484084729, 3.01452354997332, 2.77287003780052, 
Inf, 2.7977945011341, 2.13125024502472, 2.00231645203565, 3.17676858662151, 
2.250850130045, 4.56438346167388, 3.74192333302239, 2.64720514366221, 
2.08529284408902, 2.06542689864352, 2.60689052694399, 2.20074196429853, 
2.66360471672167, 3.68046996998894, 2.04521143865008, 2.88391771167986, 
2.14304181480205, 2.05638443881326, 2.24282957640845, 2.5863365146746, 
2.18660101722396, 2.78182178917644, 2.55421505591909)), row.names = c(NA, 
-200L), class = c("data.table", "data.frame"), .internal.selfref = <pointer: 0x00000204c7761ef0>)

Answer 1

I think I found the issue, I was removing the rows with log2foldchange == Inf or -Inf from the up and down regulated lists in R, but they were still present in the unfiltered list I was doing the Excel filtering with. It appears these remained in the down-regulated lists because they were being turned into 0s, but they were being turned in NaNs in the up-regulated lists and being thrown out by Excel. I will update my answer when I have more details, but everything seems to be working well now. Thanks!