http://arxiv.org/pdf/1301.5277v2.pdf may be of interest

voom() transforms everything to log2(RPM) before estimating mean-variance
trends, so fractional count estimates from RSEM won't impact the modeling
anyhow.  See also

http://www.statsci.org/smyth/pubs/VoomPreprint.pdf

Personally I've wondered for a long, long time why people spend so much
time on GLMs for sensitivity, when more biological replicates would make
more difference.




On Mon, Aug 19, 2013 at 1:44 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi,
>
> On Mon, Aug 19, 2013 at 11:17 AM, Alan Smith <alan.sm310@gmail.com> wrote:
> > Hello,
> >
> > I used RSEM to extract gene and transcript level read count information
> for
> > our single end read libraries. Then rounded off the expected read counts
> to
> > use for differential expression analysis using edgeR at both transcript
> and
> > gene level. However, I found that the number of DE transcripts were
> almost
> > 10 times less than those of genes.
> >
> >  Is this expected or should I be following other package to analyze
> > transcript level DE analysis.
>
> If you take a minute to take a walk down memory lane and browse
> through the list archives searching for "RSEM":
>
>
> http://search.gmane.org/?query=rsem&author=&group=gmane.science.biology.informatics.conductor&sort=date&DEFAULTOP=and&xP=Zrsem&xFILTERS=Gscience.biology.informatics.conductor---A/
>
> You'll find that RSEM output doesn't play well with edgeR and DESeq.
> These methods explicitly require *count* data -- not any old number
> that has been then rounded to an integer.
>
> I recall a thread about how voom would likely work well with RSEM
> output, but I can't seem to dig it up right now -- I'm only finding
> other people mentioning that thread ;-)
>
> HTH,
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech
>
> _______________________________________________
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> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
*He that would live in peace and at ease, *
*Must not speak all he knows, nor judge all he sees.*
*
*
Benjamin Franklin, Poor Richard's
Almanack<http://archive.org/details/poorrichardsalma00franrich>

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