[BioC] shan

[Steve Lianoglou]

Hi Shan,

On Mon, Oct 1, 2012 at 1:30 PM, wang peter <wng.peter at gmail.com> wrote:
> dear ALL:
>      i want to find DE genes between two conditions,
> each condition has 6 samples, but among those 6 samples,
> 3 samples contains  51 bp reads and 3 samples contains 100 bp reads.
> that is because 51 bp reads are too short, so we sequenced
> 100 bp on the same samples.
>      i know using DESeq, i should combine 51 bp with 100 bp reads
> on each sample as technical replicate. but i donot want to remove
> those difference by combination of them.
>     who can help me design a good experimental design?

This is a somehow interesting situation ... no answers from me, but I
do have some questions :-)

Have you done some exploratory analysis to see what kind of effects
you get from different read sizes?

For example, you might try to cluster the samples to see if they
cluster by sample or by read length? Or in edgeR you can try the
plotMDS function?

Also -- did you use a "splice-aware" aligner (like tophat2, GSNAP, ...), or?.

-steve

-- 
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