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Question: why the logFC is different between edgeR,DESeq2 results and fpkm logFC(log2(FPKM_tumor_mean/FPKM_normal_mean)?
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gravatar for ZihaoXing
12 weeks ago by
ZihaoXing0
ZihaoXing0 wrote:

   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 ?

ADD COMMENTlink modified 12 weeks ago by Gordon Smyth35k • written 12 weeks ago by ZihaoXing0
1

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.

ADD REPLYlink written 12 weeks ago by Udi Landau30

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

ADD REPLYlink written 12 weeks ago by ZihaoXing0
1
gravatar for Gordon Smyth
12 weeks ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

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.

ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by Gordon Smyth35k

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

ADD REPLYlink written 12 weeks ago by ZihaoXing0
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