[BioC] Estimating Size Factors in DESeq Package

Steve Lianoglou mailinglist.honeypot at gmail.com
Sat Sep 8 01:09:18 CEST 2012

Hi Tim,

On Fri, Sep 7, 2012 at 5:45 PM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
> Hi Simon,
> I have a distantly related question -- suppose we wanted to compute FPM,
> i.e. fragments per million, for paired-end RNAseq data.  Like, say, if a
> person (me) was really really lazy and was less concerned about
> sensitivity, since they were just going to feed everything to voom() or fit
> robust linear models of log(RPM/FPM) against predictive factors.
> Is this (fragment-level computation) possible in an existing Bioconductor
> package at this point in time?  Or using HTseq, for that matter?

Are you forgetting the K (eg. FP(K)M)?

If not, I guess I'm missing something, because it's easy to compute
from a count matrix you've jimmy'd together (cf. edgeR::cpm w/

Or, are you asking how to create such a count matrix with PE data?


Apologies if I'm totally in the woods, here.


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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