Question: How to normalize mouse gene 1.0st arry using frma?
0
gravatar for aritra
2.5 years ago by
aritra0
Bose Institute, Kolkata, India
aritra0 wrote:

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 • 528 views
ADD COMMENTlink modified 20 months ago by emacreamoinn0 • written 2.5 years ago by aritra0
Answer: How to normalize mouse gene 1.0st arry using frma?
0
gravatar for Matthew McCall
2.5 years ago by
United States
Matthew McCall830 wrote:
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.
ADD COMMENTlink written 2.5 years ago by Matthew McCall830

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!

ADD REPLYlink modified 20 months ago • written 20 months ago by emacreamoinn0
Answer: How to normalize mouse gene 1.0st arry using frma?
0
gravatar for emacreamoinn
20 months ago by
emacreamoinn0 wrote:

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!

ADD COMMENTlink written 20 months ago by emacreamoinn0

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.

ADD REPLYlink modified 20 months ago • written 20 months ago by Guido Hooiveld2.5k

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.

ADD REPLYlink written 20 months ago by Matthew McCall830
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