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. Thanks! -Abhi 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > 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 > -- > www.bioinformaticstutorials.com