tximport --> edgeR

Question

[u3005992]

Hi all,

May I ask, if I am going to follow tximport data with edgeR, for tximport:

"Summarization using the abundance (TPM) values?"------ i) No, ii) scaled up to library size, iii) scaled using the avg. transcript length over samples and then the library size, iv) scaled using the median transcript length among isoforms of a gene, and then library size.

which one should I use before proceeding to edgeR?

James

Answer 1

[ATpoint]

Simply follow the manual: https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#edger The default is "no" and this is what you should use if you want to aggregate to the gene level.