counts in rna-seq cpm

Question

[vm.higareda]

hello

I am conscious that there are different programs to detect differential expression in transcriptome data, but would be correct if I compare the cpm of the same gene between different treatments, only to have an idea about the variance betwen genes.

I can use de cpm function of edgeR

What do you think?

[Kevin Blighe]

Hello, please try to explain better what you are trying to do. cpm() will normalise whatever data you supply to it - you can then easily determine gene-wise variance using the var() function, or, better, summarise the variance (rather, covariance) using principal components analysis.

[vm.higareda]

I would like to take a look of counts of one specific gene along different treatments so I think that could be better do it using the cpm not the raw counts. What do you think?

The idea is detect outlier counts in a specific gene not it all the treatment

[Kevin Blighe]

Well, yes, it is always better to use normalised counts.If you are interested in a particular gene, why not just do a differential expression analysis?

[vm.higareda]

I did differential expression analysis with edgeR and Deseq, but I would like to compare one gene along different treatments not only pairwise comparison. I am confused how to do that

[Kevin Blighe]

Would something like this help for the experimental setup that you have: https://support.bioconductor.org/p/95602/#95633