Question: What are all the different methods available for identifying the DEG?
gravatar for mathavanbioinfo
23 months ago by
mathavanbioinfo10 wrote:

Dear All, 

I am working on Micro-array data analysis  with this GEO acc no. GSE31747, In this paper PMID 22024983 ( they have used ANOVA method to identify the significant genes,Now i am  trying to compare their results with Limma package but i am not getting any single significant genes(P-Value<0.05 ). So can any one tell me if Limma not give any significant genes what else other methods i can go.


Mathavan M

Research Scholar Centre for Bioinformatics

Pondicherry University

ADD COMMENTlink modified 23 months ago by Gordon Smyth35k • written 23 months ago by mathavanbioinfo10
gravatar for SamGG
23 months ago by
SamGG160 wrote:


IMHO, the number of subjects is too small in order to get any nor general insights.

When looking for differential genes concerning INFECTION vs MOCK, there is only one reported[FINF])%20AND%20GDS4356[ACCN]. If INFECTION vs MOCK is your interest, limma gave you the right answer.


ADD COMMENTlink written 23 months ago by SamGG160
gravatar for Gordon Smyth
23 months ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

This data set clearly cannot be analyzed by a single factor ANOVA. It requires a two way approach with adjustment for donor affects. There is very little differential expression in this data apart from the large differences between the three donors. Nevertheless, when I analyzed this data in limma, I had no trouble with finding a few genes with P=2E-6 and FDR=0.004.

As far as I know, there is no valid statistical test with more sensitivity than the limma approach.

I would treat the reported results in the Wahl-Jensen et al article with a great deal of caution. It is not clear to me how they did the statistical analysis and there is no indication that they made any adjustment for multiple testing. Many or most of the DE results they report might not be reproducible.

ADD COMMENTlink modified 23 months ago • written 23 months ago by Gordon Smyth35k

Thank you for your reply, Can u send me R Code(limma)

ADD REPLYlink written 23 months ago by mathavanbioinfo10

Contributions to the support site are meant to help with your analysis, not to do it completely for you. If you need to analyze it completely from scratch, and you don't know how to do it, you should (a) have a closer look at the limma user's guide, especially the case studies; or preferably (b) consult/collaborate with a local bioinformatician.

ADD REPLYlink modified 23 months ago • written 23 months ago by Aaron Lun21k
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