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Question: can i only analyse some genes different RNAseq expression analyse not the whole transcriptome RNAseq analyse by DESeq2 or edgeR
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gravatar for ZihaoXing
4 weeks ago by
ZihaoXing0
ZihaoXing0 wrote:

I only want to analyse some genes different RNAseq analyse ,if i analyse the whole transcriptome genes ,it will cost a long time ,and i found if the gene numbers i analysed are different ,the p value and FDR results are also different.

ADD COMMENTlink modified 4 weeks ago by Gordon Smyth35k • written 4 weeks ago by ZihaoXing0

Why is the analysis taking a long time? Because of a huge number of samples? Some other reason?

ADD REPLYlink written 29 days ago by Gordon Smyth35k

yes,sample number is huge,and the whole genome analyse cost a long time , especially  of edgeR.

ADD REPLYlink written 29 days ago by ZihaoXing0
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gravatar for Gordon Smyth
4 weeks ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:

You can theoretically analysis just a handful of genes, but normalization as well as the empirical Bayes strategies that make edgeR and DESeq2 so powerful work best if you analyse the whole genome. The usual procedure is therefore to analyse everything and then just look at the results of interest at the end.

We find that edgeR works acceptably even on tens of thousands of samples. But, if you find edgeR too slow, then use limma.

If you have a huge number of samples then empirical Bayes becomes far less important. In that case, you could normalize using the whole genome and then run the DE analysis just for your genes of interest.

ADD COMMENTlink modified 29 days ago • written 4 weeks ago by Gordon Smyth35k

thanks a lot for your reply, DESseq2 cost more time than edgeR, you say analyse the whole genome can make a better results. some times ,i think that if i need to analyse the whole genome to see a few of genes analyse results ,it is not very convenient.

ADD REPLYlink modified 29 days ago by Gordon Smyth35k • written 29 days ago by ZihaoXing0
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