tximport --> edgeR
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
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u3005992 •
1 answer
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.
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