[BioC] Goseq plot

[Alicia Oshlack]

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 at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] Goseq plot
> Message-ID:
> <CAO0xdQPci-DNtU+yckAFuF6h5WDJoFj954Ot+KtrtO_ngu=xFA at 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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