Bioconductor - Mogene10Stv1Mmensgcdf Not Available -Rma(Affybatchobject)

Question

[Agatha]

I have loaded an affyBatch object via R and I am encountering issues when assigning the CDF environment

set <- ArrayExpress(input="E-MEXP-2802")
norm.full<-rma(set) 
set@cdfName<-paste("MoGene-1_0-st-v1-Mm-ENSG") # assign cdf

Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain MoGene-1_0-st-v1-Mm-ENSG Library - package mogene10stv1mmensgcdf not installed Bioconductor - mogene10stv1mmensgcdf not available

I have tried to install the mogene10stv1mmensgcdf package from different mirrors or saved locally on my computer from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp.

Error: (..) is not available (for R version 2.15.1)

I have updated R from 1.15.0 and the installed packages (on MacOs) . I have also tried in windows as well, R 2.14. Nothing seems to work..

Is there perhaps an alternative to this?

SessionInfo:

> sessionInfo()

R version 2.15.1 (2012-06-22) Platform: x8664-apple-darwin9.8.0/x8664 (64-bit)

locale: [1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets  methods   base     

  other attached packages:
[1] mogene10stv1cdf_2.10.0 affy_1.34.0            ArrayExpress_1.16.0    AnnotationDbi_1.18.1  
[5] Biobase_2.16.0         getopt_1.17            Biostrings_2.24.1      IRanges_1.14.4        
[9] BiocGenerics_0.2.0     gridExtra_0.9          ggplot2_0.9.1          BiocInstaller_1.4.7

[ 13] cluster1.14.2 R2HTML2.2 plyr1.7.1 nnet7.3-4
[17] nlme3.1-104 DBI0.2-5

 loaded via a namespace (and not attached):

[1] MASS7.3-19 RColorBrewer1.0-5 RSQLite0.11.1 XML3.9-4 affyio1.24.0
[6] colorspace1.1-1 dichromat1.2-4 digest0.5.2 labeling0.1 lattice0.20-6
[11] limma3.12.1 memoise0.1 munsell0.3 preprocessCore1.18.0 proto0.3-9.2
[16] reshape21.2.1 scales0.2.1 stats42.15.1 stringr0.6 tools2.15.1
[21] zlibbioc_1.2.0

[Duff]

Hi Agatha

More information would be useful (e.g. sessionInfo() output, some details on how the AffyBatch was created?) but for the record if you're trying to use the 'affy' package then it won't work for the Gene ST array - which I presume you're using from the CDF you are trying to load. If this is the case you need the oligo or xps packages.

Best

iain

[Agatha]

Hi, I have edited my post with extra info. I am trying to assign the ensg cdf to the data downloaded from ArrayExpress. I ve had this code working while ago and I have worked on the same data set...I am not sure what couses this incompatibility.Thanks.

Answer 1

[Duff]

Hi Agatha

I use linux not a mac but the following worked for me. Download the mogene10stv1mmensgcdf_15.1.0.tar.gz from the Brainarray website, open Terminal and change directory (cd) to the directory you downloaded the file into. Then type

R CMD INSTALL mogene10stv1mmensgcdf_15.1.0.tar.gz

That should install the cdf for R to use.

Open R and type

library(AffyExpress)
library(mogene10stv1mmensgcdf)
set <- ArrayExpress(input="E-MEXP-2802")
norm.full<-rma(set)
set@cdfName <- 'mogene10stv1mmensgcdf'

As I say this worked for me. I note from your sessionInfo() above that you didn't have the cdf package loaded - perhaps that was the problem.

HTH

best

iain

[Agatha]

Hi Iain! I have tried this as it is under Linux and it works. However, it didn't work on Mac. I am not sure why is this happening. I have managed to get this to work on Windows as well, with R.14, and mogene10stv1mmensgcdf version 14. I will post my answer as well if I will be able to make it to work on Mac. It doesn't make any sense ..Thank you! Best, Agatha

[Duff]

Hi Agatha

It might be best to ask about this on the bioconductor mailing list. You can sign up on the bioconductor website and there are many people there who know more about bioconductor than I do.

I have a mac at home so I'll try it out there and see what happens.

Best

Iain

[Agatha]

Hi Iain, in my case the main problem was RStudio...I realized that when I was not able to install some random bioconductor packages...I have installed them from the command line and then I have loaded them and it worked..And the main problem is that in my case Rstudio doesnt give access to several websites(eg brainarray) containing annotations or similar causing a broken/completely failed installation. Best, Agatha