Found the same thing
Hey All,
I noticed the same thing as konrad98 a while ago. I ran CuffDiff and DESeq on 2x36 bp PE-Reads from replicate samples. Cuffdiff says that ~30% are differentially expressed, whereas DESeq found 0. To find out why, I made MA plots for my samples. The X-axis is the average RPKM for the two samples and the Y-axis is the log2 Fold Change.
As you can see, CuffDiff (for some reason) is much more variable in its calculation of RPKM. Note, these are the RPKM values from the genes.expr file and gene-level counting in exons.
Hey All,
I noticed the same thing as konrad98 a while ago. I ran CuffDiff and DESeq on 2x36 bp PE-Reads from replicate samples. Cuffdiff says that ~30% are differentially expressed, whereas DESeq found 0. To find out why, I made MA plots for my samples. The X-axis is the average RPKM for the two samples and the Y-axis is the log2 Fold Change.
As you can see, CuffDiff (for some reason) is much more variable in its calculation of RPKM. Note, these are the RPKM values from the genes.expr file and gene-level counting in exons.
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