frma: "mogene.2.0.stfrmavecs" availability?? - Gene Barcode 3.0
1
0
Entering edit mode
minnie • 0
@minnie-9570
Last seen 5.6 years ago

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 • 891 views
ADD COMMENT
0
Entering edit mode
@matthew-mccall-4459
Last seen 2.3 years ago
United States

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 COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 242 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6