How to normalize mouse gene 1.0st arry using frma?
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aritra • 0
@aritra-7091
Last seen 6 months ago
Bose Institute, Kolkata, India

Hello,

I wanted to normalize an affy mouse gene 1.0 ST array using frma method. I get the following error:

package ‘mogene10stv1frmavecs’ is not available (for R version 3.1.1).

How to solve this?

microarray frma • 790 views
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@matthew-mccall-4459
Last seen 2.4 years ago
United States
Please make sure you have installed the mogene.1.0.st.v1frmavecs package and that you've read in the data using the oligo package.
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Unfortunately, I'm running into the same problems and haven't been able to apply the fRMA method to many Affymetrix GeneChip, including Mouse Genome 430A 2.0, Mouse Exon 1.0 ST Array, MOE430A, and MOE430B. When I try to install the necessary packages, I continue to get the following warning "package ‘XXX’ is not available (for R version 3.3.1)".

I have tried installing older versions of R, but this hasn't helped.

Is there any way around this? Thank you in advance for your help!

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@emacreamoinn-15156
Last seen 3.7 years ago

Unfortunately, I'm running into the same problems and haven't been able to apply the fRMA method to a number of Affymetrix genechips, including Mouse Genome 430A 2.0, Mouse Exon 1.0 ST Array, MOE430A, and MOE430B. When I try install the necessary packages I continue to get the following warning "package ‘XXX’ is not available (for R version 3.3.1)".

I have tried installing older versions of R but this hasn't helped.

Is there anyway aroudn this? Thank you in advance for your help!

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Basically the message tells you what is going on: for the current version of Bioconductor (R-3.4.x) only 3 predefined frozen RMA vectors are available for mouse arrays, i.e. mogene.1.0.st.v1frmavecs, mouse4302frmavecs, and mouse430a2frmavecs. For the arrays you mention these vectors/info isn't available. Main reason (I believe) is that it takes some (manual) effort to generate these (you will need a large database of biologically diverse samples from a variety of batches, e.g. from GEO). If you would like to go that way, see the package frmaTools here. This also holds true for older versions of Bioconductor.

This thread also relates to your question: A: fRMA normalization for Mouse Gene 2.1 ST Array.

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Guido is correct that the bottleneck is manual curation of public data and estimation of the frozen parameter vectors. For newer platforms, there may simply not be enough public data available yet. I aim for 1000 samples across 200 experiments. I do keep a mental tally of requests for frmavectors for different platforms and when I have time, I try to implement frma on new platforms.

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