Question

DEG test for two closely related conditions with limma

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Shamim Sarhadi ▴ 20

@shamim-sarhadi-9395

Last seen 7.3 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 • 1.2k views

ADD COMMENT • link updated 8.1 years ago by Aaron Lun ★ 28k • written 8.1 years ago by Shamim Sarhadi ▴ 20

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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

ADD REPLY • link 8.1 years ago Shamim Sarhadi ▴ 20

score 0 · Answer 1 · 2016-03-18

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.