Thanks very much Belinda. That is comforting.

My DGEList object has library sizes added to it. Do I still need to supply
a numeric vector with library sizes while fiting glm? Or is it
automatically pulled from DGEList object?

Reading help, i understand its automatic. Please advice me if I am wrong.
" If y is a DGEList object then the default for lib.size is the product of
the library sizes and the normalization factors (in the samples slot of the
object). "

Thanks,
Gowthaman




On Thu, Jun 21, 2012 at 4:58 PM, Belinda Phipson <phipson@wehi.edu.au>wrote:

> Hi Gowthaman
>
> Your output looks fine. What is more important is that library size is
> taken into account as an offset later on when you fit the glm. See
> help(glmFit).
>
> Cheers,
> Belinda
>
> -----Original Message-----
> From: bioconductor-bounces@r-project.org [mailto:
> bioconductor-bounces@r-project.org] On Behalf Of gowtham
> Sent: Friday, 22 June 2012 9:40 AM
> To: bioconductor
> Subject: Re: [BioC] edgeR: calcNormFactors question
>
> Sorry about repeated mailing: I have attached a smear plot of the data
> incase that helps anyone attempting to answer my doubt.....
>
>
> On Thu, Jun 21, 2012 at 4:07 PM, gowtham <ragowthaman@gmail.com> wrote:
>
> > Hi Everyone,
> > I am analyzing a RNAseq experiment with two groups each having two
> > replicates. One out of 4 libraries have only half as much reads
> > mapping to genome.
> >
> > Lib Fe+.1 has only 4 million reads while other are 9 million +. But
> > still the norm.factors are not much different. With my naive
> > understanding i expect Fe+.1 to be very different from others. I would
> > like to know if what I see is okay?
> >
> > > oldsetDGE <- calcNormFactors(oldsetDGE) oldsetDGE$samples
> >       group lib.size norm.factors
> > fe-.1     2  9664343    0.9865411
> > fe-.2     2 11248827    1.0812947
> > fe+.1     1  4194124    0.9662389
> > fe+.2     1  9963626    0.9701888
> >
> >
> > Thanks very much,
> > Gowthaman
> > --
> > Gowthaman
> >
> > Bioinformatics Systems Programmer.
> > SBRI, 307 West lake Ave N Suite 500
> > Seattle, WA. 98109-5219
> > Phone : LAB 206-256-7188 (direct).
> >
>
>
>
> --
> Gowthaman
>
> Bioinformatics Systems Programmer.
> SBRI, 307 West lake Ave N Suite 500
> Seattle, WA. 98109-5219
> Phone : LAB 206-256-7188 (direct).
>
>
> ______________________________________________________________________
> The information in this email is confidential and inte...{{dropped:20}}

