Question: frma: "mogene.2.0.stfrmavecs" availability?? - Gene Barcode 3.0
0
gravatar for minnie
3.8 years ago by
minnie0
minnie0 wrote:

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!

 

 

frma affymetrix barcode • 635 views
ADD COMMENTlink modified 3.8 years ago by Matthew McCall830 • written 3.8 years ago by minnie0
Answer: frma: "mogene.2.0.stfrmavecs" availability?? - Gene Barcode 3.0
0
gravatar for Matthew McCall
3.8 years ago by
United States
Matthew McCall830 wrote:

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

ADD COMMENTlink written 3.8 years ago by Matthew McCall830

Thank you very much for the reply! I realized after reading the paper/website in detail that it was not yet available. I'd be happy to help, but I am not sure if I am really capable since I am still a newbie in terms of coding in R.

ADD REPLYlink written 3.8 years ago by minnie0

As I mentioned, the main bottleneck is curation of the sample annotation (the R coding is basically done). Curation means examining the annotation in the GEO SOFT files, and if the annotation is missing or unclear, going back to the original paper to find out what the samples really are (e.g. liver tumor cells treated with drug X). If you are interested in helping with this, send me an email and I'll put you in touch with the person who coordinates these efforts.

Best, Matt

ADD REPLYlink written 3.8 years ago by Matthew McCall830
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