[BioC] Limma Voom R package

[Wei Shi]

Dear Pedro,

You'll need to align your fastq data, summarize read counts to genes and then run limma voom or edgeR for expression analysis.

We have developed a pipeline for doing this which allows you to complete the entire analysis in R. This pipeline starts with using Rsubread package for alignment (see Rsubread vignette for more details, but briefly the functions 'buildindex' and 'align' are used for index building and read mapping, respectively), and then uses featureCounts function in the same package to do the read summarization. The summarized read counts can then be fed into limma or edgeR for expression analysis.

Cheers,
Wei

On Jan 8, 2013, at 7:47 AM, Pedro Blecua wrote:

> Dear Sir/Madam,
> 
> I am a postdoctoral researcher at Chris Mason's lab at the ICB Cornell
> Medical College in NYC.
> I would be very interested in using your R package for RNA-seq
> analysis of some raw data we have.
> We went through the manual quickly, and it is not clear for me how to
> start the analysis, i.e., input file.
> 
> To be more specific: given the fastq file (or binary fastq.tbz), could
> we use it as input for Voom, and then
> use the result for Limma? Or should we align first our raw fastq data
> and then use the sam or bam files as
> input for the Vomm or Limma packages? How should I proceed to start an
> analysis from raw fastq files?
> 
> I would highly appreciate an answer at your earliest convenience.
> 
> Thank you very much in advance for your attention,
> 
> 
> -- 
> Best,
> 
> Pedro
> 
> Pedro Blecua, Ph.D.
> Postdoctoral Associate
> Weill Medical College of Cornell University
> Institute for Computational Biomedicine
> Department of Physiology and Biophysics
> 1305 York Avenue, Box 140,
> New York, NY 10021
> 
> Office: 212 746 4237
> Fax:    212 746 8690
> 
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