Comparing expression of DEG gene in samples

Question

[Maryam]

Hi, I got the DEG table with the limma package in R, I searched for the SNAI1 gene in the DEG table and now I want to compare my gene expression in the samples. I want to know in which samples SNAI1 is up-regulated and in which samples it is reduced. How can I do that? With what code?

 library(edgeR)
library(limma)
dge <- DGEList(rawdata)
keep <- filterByExpr(dge, design = design)
keep2 <- data.frame(keep)
filt <- dge[keep, ,keep.lib.size = F]
norm <- calcNormFactors(filt, method = "TMM")
v <- voom(norm, design = design, plot = T)
E <- v$E
ex <- 2^E
Ex <- log2(ex + 1)


##DEG using edgeR and limma##

fit <- lmFit(Ex, design = design)
contrast <- makeContrasts(cancer-normal, levels = design)
fit2 <- contrasts.fit(fit = fit,contrasts = contrast)
fit2 <- eBayes(fit = fit2)  
diff <- topTable(fit = fit2, number = Inf, sort.by = "P" ) 

[kashiff007]

have you read the manual of limma/edgeR/DEseq2 etc?

[Maryam]

Well I took a quick look at limma and adgeR in doing 'Differentially Expressed Genes' but I did not read carefully. I should read carefully .Thanks