Question: How to extract common genes that are DE in each comparisons?
1
gravatar for rkpathakbt
2.2 years ago by
rkpathakbt10
India
rkpathakbt10 wrote:

I have made a Contrasts matrix as

design <- model.matrix(~0+f)
colnames(design) <- levels(f)
design
fit <- lmFit(eset,design)
names(fit)
cont.matrix <- makeContrasts(C9T9="Control9-Treated9",C24T24="Control24-Treated24",........................................,levels=design)
cont.matrix
fit2  <- contrasts.fit(fit, cont.matrix)
fit2  <- eBayes(fit2)
colnames(fit2)
topTable(fit2,coef=1)
topTable(fit2,coef="C9T9")

I have total of 8 comparisons and successfully extracted up and down-regulated genes from each comparisons using topTable, beside also identified the total number of up and down-regulated genes from each comparisons using

summary(decideTests(fit2))

but I am facing problem to identify/extract common genes that are DE in each of comparisons. Therefore, It is my kind request to all of you, please provides any suggestions for extracting of common genes that are DE in each of the comparisons.

Thanking you.

Kind regards,

ADD COMMENTlink modified 2.2 years ago by genomax64k • written 2.2 years ago by rkpathakbt10

Hello rkpathakbt!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/91399/

This is typically not recommended as it runs the risk of annoying people in both communities.

ADD REPLYlink written 2.2 years ago by WouterDeCoster37k

Ok, Thanks for this information.

ADD REPLYlink written 2.2 years ago by rkpathakbt10
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