Microrna Chip Analysis Using Bioconductor

Question

[rarzate89]

Hi everyone:

I just got some mirna data form the miRNA 2.0 array by affymetrix. My problem is that while working with the gcrma normalization I got this message:

celfiles.gcrma<- gcrma(celfiles)
Adjusting for optical effect....Done.
Computing affinities[1] "Checking to see if your internet connection works..."
[1] "Environment mirna20probe was not found in the Bioconductor repository."
Error in get(probepackagename) : object 'mirna20probe' not found

I was wondering if someone have an idea of how to overcome this issue.

Thanks! Rodrigo

Answer 1

[Neilfws]

The error means what it says: Bioconductor does not have a probe package for that array platform. See this mailing list answer. So you cannot use gcrma in this case.

You might be able to use Affymetrix' own software, Affymetrix Power Tools. There is also a Bioconductor annotation package for the platform, so some other kind of normalization using Bioconductor may be an option.