[BioC] Analysing RNA-Seq data using DESeq package

[Steve Lianoglou]

Hi Suryavadhan,

On Tue, Sep 13, 2011 at 12:41 PM, Kayilai, Suryavadhan (MU-Student)
<skhx5 at mail.missouri.edu> wrote:
> I downloaded the DESeq package for the RNA seq analysis of the Soybean genes. The package is really helpful and easy to use. Thanks! I have a small doubt and it would be kind of you, if could help me figure out the same.
>             The package works fine for the gene data with whole number or integer values. How can I run the analysis for decimal data as the class newCountDataset does not allow me to input decimal data. It would be great if you could help me through this.

It doesn't let you put in non-integer data, because the models DESeq
uses to test for significance assumes count data -- as in, the number
of reads that align to a given region, which can only ever be
integers.

What types of data are you trying to put in that are decimal values,
anyway? What does it represent?

-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