hi Dvir

I am not familiar with RSEM software, but you have non-integer values in
the raw_count column, for example 31.95 and 258.35.  Non-integer values are
not appropriate for DESeq or edgeR analysis.

Searching for a minute on Google it seems that these raw counts involve
assigning fractions of ambiguously mapped reads (but you should check with
the RSEM developers).  If you don't have access to any lower level data,
the next best option is to round the raw_count values and proceed.

best,

Mike

On Wed, Mar 20, 2013 at 2:15 PM, <dvir.tau@gmail.com> wrote:

> Hello,
>
>
>
> I'm running DESeq and EdgeR on RNA-Seq data that was already processed with
> RSEM (downloaded from TCGA web site).
>
> Since these methods require the raw read counts I'm using the raw_count
> column of the RSEM output but I'm not sure this is the right thing to do
> (is
> it the actual raw count required ?)
>
>
>
> Here's an example file for the RSEM output file downloaded from TCGA:
>
>
>
>
> barcode
>
> gene_id
>
> raw_count
>
> scaled_estimate
>
> transcript_id
>
>
> TCGA-A1-A0SB-01A-11R-A144-07
>
> ?|100130426
>
> 0
>
> 0
>
> uc011lsn.1
>
>
> TCGA-A1-A0SB-01A-11R-A144-07
>
> ?|100133144
>
> 34.05
>
> 1.23812E-06
>
> uc010unu.1,uc010uoa.1
>
>
> TCGA-A1-A0SB-01A-11R-A144-07
>
> ?|100134869
>
> 31.95
>
> 8.40876E-07
>
> uc002bgz.2,uc002bic.2
>
>
> TCGA-A1-A0SB-01A-11R-A144-07
>
> ?|10357
>
> 258.35
>
> 2.16969E-05
>
> uc010zzl.1
>
>
> TCGA-A1-A0SB-01A-11R-A144-07
>
> ?|10431
>
> 1459
>
> 5.53441E-05
>
> uc001jiu.2,uc010qhg.1
>
>
>
>
>
> Many thanks,
>
> Dvir
>
>
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>
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