Hi Alicia,

I checked the length annotation, it was fine. Also I looked at the pwf plot
for counts bias, it looks even flatter
(no bias). But I was wondering why there are only a few points on the plot,
if we looking at gene length vs proportion of DE genes?
As I mentioned in the previous email, I have 1802 DE genes and 28771 nonDE
genes in my samples.

Here is the plot for the count bias.

https://docs.google.com/open?id=0B_mk9qnFziV-aEhjeGZsY3BSVC1tMWUwTElzWENXQQ


Thanks,
Al



On Sun, Feb 26, 2012 at 4:49 PM, Alicia Oshlack
<alicia.oshlack@mcri.edu.au>wrote:

> Hi Al,
>
> To me the plot looks like a perfectly good fit to the data. The thing is
> that it doesn't look like there is much gene length bias in the plot that
> you have shown. I'm not really sure why this would be as it is usually a
> strong effect but perhaps the biological signal is even stronger than this
> technical effect? You might just want to check the matching of your gene
> length annotation to DE genes, just in case.
>
> Cheers,
> Alicia
>
> > From: Alpesh Querer <alpeshq@gmail.com>
> > To: bioconductor@r-project.org
> > Subject: [BioC] Goseq plot
> > Message-ID:
> > <CAO0xdQPci-DNtU+yckAFuF6h5WDJoFj954Ot+KtrtO_ngu=xFA@mail.gmail.com>
> > Content-Type: text/plain
> >
> > Hi Goseq ers,
> >
> > I followed the user manual for Goseq and came up with the following
> plot, I
> > am working with corn data, so
> > I imported the lengths from Biomart and manually created the annotation.
> > Can you please guide me if the Pwf plot is a good fit for my data,
> > also is there a way to find which of  gene-length and counts to use as
> > bias.data. The plot is for gene length bias.
> > I have 1802 DE genes and 28771 nonDE genes in my samples (edgeR output) .
> > Also if the plotPWF function plots
> > the pwf values, why only a handful of values can be seen in this plot?
> > Please pardon my statistical ignorance.
> >
> >
> https://docs.google.com/open?id=0B_mk9qnFziV-SHE0LXQ0ZUFUb0dNMEEzN1UwVGhjQQ
> >
> > Many Thanks,
> > Al
> >
>
>
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