DEG analysis by limma

Question

[Shamim Sarhadi]

Hi

I have analyzed DEG between control vs sensitive to drug X, control vs insensitive to drug X, and sensitive vs insensitive. I used limma to find related DEGs, here is my code

fit <- lmFit(data, design)
keep <- fit$Amean > median(fit$Amean)
ebayes <- eBayes(fit[keep,], robust=TRUE, trend=TRUE)
tab <- topTable(ebayes, coef=2, adjust="BH",n=100)
colnames(design)

[1] "(Intercept)"                                            "factor(sensitivity$chemosensitivity)Rx Sensitive"

Now from limma output, I found genes with negative log fold change that are express higher in the insensitive samples and genes with positive log fold changes that are express higher in the sensitive samples, but, what I want to know is down regulated genes in each phenotype

[Caitlin]

Hi Shamim.

I realize this is quite late, but did you solve this issue? If so, could I ask you for help with a project?

Thank you.

~Caitlin

[Kevin Blighe]

It is likely that the factor levels are not in the order that you assume. Which comparison do you want to perform? Please show the output of str(design)