Question: How can I compare the expression of two genes within the same sample?
0
gravatar for chiara.facciotto
10 weeks ago by
chiara.facciotto0 wrote:

Hi,

I am interested in comparing the expression of genes within the same sample and ranked them from the most expressed to the least expressed. I cannot use counts nor normalized counts because they do not take into account the gene lengths. Which measure would you suggest I use? Does DESeq2 provides a function to transform raw counts into such format?

rnaseq deseq2 gene expression • 109 views
ADD COMMENTlink modified 10 weeks ago by heyao30 • written 10 weeks ago by chiara.facciotto0

You can use the cqn normalization that takes into account the gene length.

ADD REPLYlink written 10 weeks ago by LluĂ­s Revilla Sancho460
Answer: How can I compare the expression of two genes within the same sample?
0
gravatar for heyao
10 weeks ago by
heyao30
heyao30 wrote:

You can transform your raw counts to FPKM or TPM (recommend) for such within-sample comparsion, as these two normalization both takes gene length into consideration.

ADD COMMENTlink written 10 weeks ago by heyao30
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