[BioC] Goseq plot

[Alicia Oshlack]

Hi Al,

Even though the spline is fit on all the data (green line) the plot is made
by binning the genes according the length or number of reads and calculating
the proportion of DE in each bin. Therefore you get fewer points than the
number of DE genes. As you know to just plot genes individually is just
plotting 1 or 0 and doesn¹t give you a feel for the proportions.

Cheers,
Alicia 


On 28/02/12 10:00 PM, "bioconductor-request at r-project.org"
<bioconductor-request at r-project.org> wrote:

> Message: 14
> Date: Mon, 27 Feb 2012 11:41:09 -0600
> From: Alpesh Querer <alpeshq at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC]  Goseq plot
> Message-ID:
> <CAO0xdQNYGpM=n5iLo4OTcUTFOTYo4UYYsG+agiv5v6dsGbGPmw at mail.gmail.com>
> Content-Type: text/plain
> 
> 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


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