Hello,

I am trying to perform analyses based on the Gene Barcode 3.0 statistical software. I have installed all the relevant packages but having an issue running the frma function since I cannot seem to download the "mogene.2.0.stfrmavecs" package. (My affymetrix data is Mouse gene 2.0. ST).

For instance:

> celFiles <- list.celfiles("~/Downloads/CEL_files")
> affyRaw <- read.celfiles(celFiles)
Loading required package: pd.mogene.2.0.st
Loading required package: RSQLite
Loading required package: DBI
Platform design info loaded.
Reading in : JS_A1_1.CEL
Reading in : JS_B6_14.CEL
Reading in : JS_D3_27.CEL
Reading in : JS_E8_40.CEL
> object=frma(affyRaw)
Error in frma(affyRaw) : 
  mogene.2.0.stfrmavecs package must be installed first
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mogene.2.0.stfrmavecs’

And when I do try installing this package, I get the following error:

> biocLite("mogene.2.0.stfrmavecs")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.2 (2015-08-14).
Installing package(s) ‘mogene.2.0.stfrmavecs’

Warning message:
package ‘mogene.2.0.stfrmavecs’ is not available (for R version 3.2.2) 

Is this package not available at all or not available for the R version 3.2.2? What version of R may I install the package?

Any help would be appreciated. Thank you in advance!

Unfortunately, frma has not been implemented for that platform yet. You could create your own frma vectors using the frmaTools package, but there also isn't a barcode implementation for that platform yet either. That platform is on the to-do list though, so there may be an implementation in the not too distant future. If you're interested in helping with the process (the main bottleneck is manual curation of the sample annotation), let me know and we may be able to speed things up a bit with your help.

Best, Matt