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  • Condition-specific genes

    Hi all,

    I have to analyze RNAseq data concerning 4 different tissues. I have biological replicates.
    Until now, I did pairwise DE analyses using edgeR and I got the Differntially Expressed genes for each comparison, with p-values and FDR.

    Now, I would like to look at the condition-specific genes but I am not sure about the way to get them...
    I can either start from the different fold-changes in the different pairwise comparisons and try to get the conditions were a gene is the most expressed, but it is quite complicated.
    I also tried to cluster the genes (after sequencing depths normalizations) but then I have the problem of genes which are not expressed at all (0 counts) in some tissue.

    I looked at some R packages like SpeCond but this one was done for microarrays so the quantification distribution is quite different and I do not think we can apply the same statistical model.

    How do you do?

    Thanks in advance...

  • #2
    It is best to build up the condition-specific genes by making comparisons between the conditions.

    Suppose you want genes that are specific to condition A. For a very stringent set, choose genes that are DE and up-regulated for all the comparisons A vs B, A vs C and A vs D.

    For a less stringent set, find genes that are DE for the contrast A - (B+C+D)/3.

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