[BioC] re incomplete analysis in Deseq

[Steve Lianoglou]

Hi Simon,

On Tue, Mar 6, 2012 at 5:38 PM, Simon Anders <anders at embl.de> wrote:
> Hi
>
>
> On 2012-03-06 22:21, Steve Lianoglou wrote:
>>
>> Couldn't we just-as-well adapt the estimateSizesFactorsForMatrix
>> function to step over the (row,col) bins that have the 0 counts
>> instead of skipping over rows that only have 1 0 element?
>
>
> This might cause a bit of a bias, as we censor data which might pull down
> data.

I'm curious if you could elaborate a bit -- maybe give a toy example
of what you mean? I'm having a hard time parsing that sentence :-)

I guess (maybe) you're talking about a scenario where bin A has a
super-high read count in expt1 but bin A has a 0 read count in expt2,
then this number will essentially be skipped when calculating the size
factors? And I guess there might be some pathological datasets where
there are many such events?

Or, am I jumping down the wrong rabbit hole, here?

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact