DEG test for two closely related conditions with limma
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@shamim-sarhadi-9395
Last seen 4.8 years ago

 

I did DEG test on two closely related conditions with limma, take a look at my output from toptable function
as you see, my logFcs are mostly less than common logFC in DEG analysis(1.5-2), do you have any idea about a cutoff or ranking my genes, and one thing else that I need to notice on, is my B values !!! 
I appreciated you if let me know your opinion about my output

 

limma DEG • 720 views
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  ENTREZID SYMBOL GENENAME logFC AveExpr t P.Value adj.P.Val B
209604_s_at 2625 GATA3 GATA binding protein 3 -1.86194 11.94945 -16.4911 1.13E-43 2.52E-39 87.80155
209602_s_at 2625 GATA3 GATA binding protein 3 -2.20487 9.878642 -14.3371 1.10E-35 1.22E-31 69.91106
209603_at 2625 GATA3 GATA binding protein 3 -2.19334 9.423654 -14.2606 2.10E-35 1.56E-31 69.28074
214164_x_at 771 CA12 carbonic anhydrase XII -1.83078 10.4947 -13.0946 3.72E-31 2.07E-27 59.75244
215867_x_at 771 CA12 carbonic anhydrase XII -1.79562 10.55449 -12.6205 1.87E-29 8.34E-26 55.93303
213693_s_at 4582 MUC1 mucin 1, cell surface associated -1.89986 10.85529 -12.4247 9.34E-29 3.47E-25 54.36628
202286_s_at 4070 TACSTD2 tumor-associated calcium signal transducer 2 -1.5046 11.51408 -11.5239 1.37E-25 4.35E-22 47.26135
214428_x_at NA C4B NA -1.83599 10.79075 -11.3592 5.08E-25 1.41E-21 45.98249
218211_s_at 79083 MLPH melanophilin -1.39848 11.40424 -11.1509 2.64E-24 6.55E-21 44.37466
209360_s_at NA RUNX1 NA -0.84908 9.784335 -11.0934 4.16E-24 9.27E-21 43.93294
213605_s_at 728093 LOC728093 putative POM121-like protein 1-like -1.29333 9.559663 -10.7888 4.52E-23 9.15E-20 41.60837
204798_at 4602 MYB v-myb avian myeloblastosis viral oncogene homolog -1.56273 9.442786 -10.74 6.60E-23 1.23E-19 41.23844
203476_at 7162 TPBG trophoblast glycoprotein -1.00429 10.26733 -10.7038 8.75E-23 1.50E-19 40.96462
202309_at 4522 MTHFD1 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase 0.59023 8.794654 10.50952 3.93E-22 6.25E-19 39.50099
218807_at 10451 VAV3 vav 3 guanine nucleotide exchange factor -1.45653 9.953283 -10.4191 7.87E-22 1.17E-18 38.82365
213627_at 10916 MAGED2 melanoma antigen family D, 2 -0.9683 10.62024 -10.4054 8.74E-22 1.22E-18 38.72135
214038_at 6355 CCL8 chemokine (C-C motif) ligand 8 1.418537 6.200059 10.37438 1.11E-21 1.45E-18 38.49003
207469_s_at 8544 PIR pirin (iron-binding nuclear protein) 1.068895 5.896498 10.33954 1.45E-21 1.79E-18 38.23032
201242_s_at 481 ATP1B1 ATPase, Na+/K+ transporting, beta 1 polypeptide -1.25314 10.61522 -10.3227 1.65E-21 1.93E-18 38.10517
201596_x_at 3875 KRT18 keratin 18 -1.12436 11.57029 -10.2463 2.95E-21 3.28E-18 37.5373
208451_s_at NA C4B NA -1.65474 11.08876 -10.2137 3.78E-21 4.01E-18 37.296
204653_at 7020 TFAP2A transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha) -1.13946 10.00996 -10.1563 5.84E-21 5.91E-18 36.8711
213110_s_at 1287 COL4A5 collagen, type IV, alpha 5 -1.6599 7.98337 -10.1271 7.29E-21 7.06E-18 36.6554
213089_at 1E+08 LOC100272216 uncharacterized LOC100272216 -1.21155 8.854537 -10.0024 1.87E-20 1.73E-17 35.73832
204508_s_at 771 CA12 carbonic anhydrase XII -1.59392 8.942029 -9.96111 2.55E-20 2.19E-17 35.43588
201243_s_at 481 ATP1B1 ATPase, Na+/K+ transporting, beta 1 polypeptide -1.11433 10.47693 -9.96043 2.56E-20 2.19E-17 35.43089
208718_at 10521 DDX17 DEAD (Asp-Glu-Ala-Asp) box helicase 17 -0.44775 12.29535 -9.95308 2.71E-20 2.23E-17 35.37717
205225_at 2099 ESR1 estrogen receptor 1 -2.10714 10.66193 -9.91405 3.63E-20 2.89E-17 35.09188
221874_at 57535 KIAA1324 KIAA1324 -1.36359 8.100067 -9.87813 4.75E-20 3.65E-17 34.82981
204058_at 4199 ME1 malic enzyme 1, NADP(+)-dependent, cytosolic 1.346521 5.620972 9.714226 1.61E-19 1.20E-16 33.64004
221899_at 10443 N4BP2L2 NEDD4 binding protein 2-like 2 -0.93522 9.537681 -9.70532 1.72E-19 1.24E-16 33.57569
200670_at 7494 XBP1 X-box binding protein 1 -0.90678 11.67877 -9.69798 1.82E-19 1.27E-16 33.52266
209341_s_at 3551 IKBKB inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta -0.85323 9.088104 -9.69241 1.89E-19 1.28E-16 33.48242
222258_s_at 23677 SH3BP4 SH3-domain binding protein 4 -0.84984 9.769341 -9.66524 2.32E-19 1.52E-16 33.28639
221728_x_at 7503 XIST X inactive specific transcript (non-protein coding) -1.0258 10.4341 -9.56091 5.01E-19 3.19E-16 32.5362
217979_at 27075 TSPAN13 tetraspanin 13 -0.66779 11.6308 -9.51838 6.84E-19 4.23E-16 32.23158
201387_s_at 7345 UCHL1 ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) 0.83655 7.1198 9.443199 1.19E-18 7.15E-16 31.69489
210835_s_at 1488 CTBP2 C-terminal binding protein 2 -0.67691 10.85555 -9.42094 1.40E-18 8.19E-16 31.5364
217499_x_at NA NA NA 0.628826 7.979557 9.416008 1.45E-18 8.28E-16 31.50132
202088_at 25800 SLC39A6 solute carrier family 39 (zinc transporter), member 6 -1.14745 11.91501 -9.40793 1.54E-18 8.56E-16 31.44387
217482_at NA NA NA -0.93503 6.602037 -9.40219 1.60E-18 8.71E-16 31.40304
202912_at 133 ADM adrenomedullin 1.238768 7.931002 9.351777 2.32E-18 1.23E-15 31.04523
202671_s_at 8566 PDXK pyridoxal (pyridoxine, vitamin B6) kinase 0.719135 8.083477 9.290526 3.61E-18 1.87E-15 30.61185
201650_at 3880 KRT19 keratin 19 -1.41407 11.40449 -9.24043 5.19E-18 2.63E-15 30.25854
218966_at 55930 MYO5C myosin VC -0.7973 9.658475 -9.1804 8.02E-18 3.97E-15 29.8365
203216_s_at 4646 MYO6 myosin VI -0.91395 9.476232 -9.14063 1.07E-17 5.17E-15 29.55774
207847_s_at 4582 MUC1 mucin 1, cell surface associated -1.6225 9.768574 -9.13677 1.10E-17 5.20E-15 29.53075
217734_s_at 11180 WDR6 WD repeat domain 6 -0.58836 9.315425 -9.06029 1.90E-17 8.82E-15 28.99668
208682_s_at 10916 MAGED2 melanoma antigen family D, 2 -0.96212 10.08932 -9.04752 2.08E-17 9.30E-15 28.90773
215304_at NA NA NA -1.46057 7.94123 -9.0471 2.09E-17 9.30E-15 28.9048
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Aaron Lun ★ 27k
@alun
Last seen 3 hours ago
The city by the bay

I don't know where you got the idea that "common log-fold change" in DE analyses is around 1.5 to 2. In my experience, log-fold changes can be anywhere from 0.5 to 10, and your results don't look too atypical. If you want to prioritize genes with larger log-fold changes, I would suggest using treat with a lfc threshold of 0.5.

Most people use a FDR threshold of 5% to define the set of DE genes, i.e., retain only those rows with adj.P.Val <= 0.05. In your case, you have plenty of genes with low adjusted p-values, so this seems suitable. As for the B-statistic, this is defined as the log-odds for DE - I don't use it much except for visualization.

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Thank you Aaron Lun

You are right,It was my mistake about lfc,Thanks for the nice comment

 

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