[BioC] help with array based microRNA data analysis

Paul Geeleher paulgeeleher at gmail.com
Mon Jan 20 19:26:11 CET 2014

Here's a previous thread that may be relevant, although I'm not sure
what you plan on doing without control samples...



On Mon, Jan 20, 2014 at 12:05 PM, Abhishek Pratap
<abhishek.vit at gmail.com> wrote:
> Hey Guys
> We have some custom array based microRNA data scanned using GenePix
> 4000B scanner and stored in gene pix results (gpr file format).
> In this case it is not necessarily case-control study as all of our
> samples are actually with the disease. Our plan is to first generate a
> simple matrix of normalized expression across all the samples.
>  To do this I would appreciate if anyone can point me to similar
> analysis/papers done in the past or Bioconductor packages that could
> help out.
> I did look at limma but not sure if it is recommended for microRNA and
> plus we dont want to do differential expression at this point.
> Thanks a lot for your time!
> -Abhi
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Dr. Paul Geeleher, PhD
Section of Hematology-Oncology
Department of Medicine
The University of Chicago
900 E. 57th St.,
KCBD, Room 7144
Chicago, IL 60637

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