Comparing expression of DEG gene in samples

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1

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? Does anyone know about this ? Thanks in advance

   library(limma)
    library(edgeR) 
    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) 

    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" )
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Hi @maryam.klntri.2695

This forum is for help using the UseGalaxy.* resources: Galaxy Platform Directory: Servers, Clouds, and Deployable Resources - Galaxy Community Hub

For help with Bioconductor packages command-line, see the package vignettes here http://bioconductor.org/ and their support forum here Bioconductor - Help.

If you want to try in Galaxy instead, or want to review those resources for general analysis guidelines/examples, see: Galaxy Training!

Thanks!