help with array based microRNA data analysis
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@abhishek-pratap-4927
Last seen 6.3 years ago
United States
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
limma microRNA limma microRNA • 879 views
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Paul Geeleher ★ 1.3k
@paul-geeleher-2679
Last seen 8.1 years ago
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
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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
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