How to extract common genes that are DE in each comparisons?

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Entering edit mode

7.9 years ago

rkpathakbt ▴ 10

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,

limma Bioiconductor R Microarray data analysis • 2.5k views

ADD COMMENT • link updated 7.9 years ago by GenoMax 147k • written 7.9 years ago by rkpathakbt ▴ 10

0

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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.