why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM_tumor_mean/FPKM_normal_mean)?
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ZihaoXing • 0
@zihaoxing-13254
Last seen 2.9 years ago

   i hava the RNAseq coutns data and fpkm data from TCGA, i want to know the fold change of tumor tissue RNAseq expression contrast of normal tissue RNAseq expression ,counts data is the RNA reads number, fpkm data is similar to real RNA expression. i found that the logFC results from DESeq2 and edgeR analyse using counts data  are different from that i use mean tumor fpkm data devide by normal fpkm data, i found that fold change  in fpkm is sifferent from the DESeq2 and edgeR fold change results . which fold cahnge  is better to choose ?

deseq2 edger fpkm counts fc • 525 views
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From what I know the fold change of edgeR and DESeq2 is calculated using normalization other than fpkm.

I would use one of edgeR or DESeq2.

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thanks Udi Landau, i will use the logFC value of edgeR or DESeq2.

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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

Your own simple logFC computation is not likely to be as good as the more sophisticated computation done by edgeR (or DESeq2).

LogFCs are computed by negative binomial generalized linear models.

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thanks Gordon Smyth, i will use the logFC value of edgeR or DESeq2 results.

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