[BioC] help with array based microRNA data analysis

Abhishek Pratap abhishek.vit at gmail.com
Mon Jan 20 22:20:52 CET 2014

Hi Paul

Appreciate your quick response. So in my case what I am looking for is
to create a matrix of expression values of these miRNA and in process
also filter out any low quality measurement. I am wondering if LIMMA
can do just that. The downstream goal is to integrate some of this
info with the miRNA-Seq data.


On Mon, Jan 20, 2014 at 10:26 AM, Paul Geeleher <paulgeeleher at gmail.com> wrote:
> Here's a previous thread that may be relevant, although I'm not sure
> what you plan on doing without control samples...
> https://stat.ethz.ch/pipermail/bioconductor/2008-May/022460.html
> Paul.
> 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
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