[BioC] Unable to perform GCRMA/RMA with cdf file 'mogene11stv1mmentrezgcdf'

[Trent Simmons]

Hi All,

I am trying to perform a GCRMA normalization of microarray data that was run on Mouse Gene 1.1 Affymetrix arrays.  I am running into an issue with the CDF file for that array (the CDF file is mogene11stv1mmentrezgcdf). 

I obtained the latest version of the CDF file from Brainarray.  When I attempted to perform the compute.affinities step, the error message:

.Error in tmp.exprs[pmIndex[subIndex]] = apm :
  NAs are not allowed in subscripted assignments

is returned.  Is anyone else experiencing this issue, or have any suggestions for how to resolve it?

I have also tried to perform basic RMA analysis using one of my CEL files and the same CDF file, just in case it was an issue solely with GCRMA.  RMA didn't work either, but in this case, it seems to be that the RMA script is looking for a CDF file called 'mogene11stv1cdf' instead.  Once again, anyone else with this issue or suggestions for a fix?


Thanks in advance,

Trent

### START CODE ###
### LOAD LIBRARIES ###
library(affy)
library(gcrma)
library(AnnotationDbi)
library(mogene11stv1mmentrezgcdf)
library(mogene11stv1mmentrezgprobe)

> ### RUN GCRMA ###
> compute.affinities('mogene11stv1mmentrezg', verbose = TRUE)
Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm :
  NAs are not allowed in subscripted assignments
>
> traceback()
1: compute.affinities("mogene11stv1mmentrezg", verbose = TRUE)

> ### RUN RMA ###
> setwd('~/Documents/test/mouse/CEL')
>
> data <- ReadAffy()
> eset <- rma(data)
Error in getCdfInfo(object) :
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain MoGene-1_1-st-v1
Library - package mogene11stv1cdf not installed
Bioconductor - mogene11stv1cdf not available
>
> traceback()
12: stop(paste("Could not obtain CDF environment, problems encountered:",
        paste(unlist(badOut), collapse = "\n"), sep = "\n"))
11: getCdfInfo(object)
10: .local(object, which, ...)
9: indexProbes(object, "pm", genenames = genenames)
8: indexProbes(object, "pm", genenames = genenames)
7: .local(object, ...)
6: pmindex(object, genenames)
5: pmindex(object, genenames)
4: .local(object, ...)
3: probeNames(object, subset)
2: probeNames(object, subset)
1: rma(data)
>
> ### SESSION INFO ###
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C             
 [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8   
 [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8  
 [7] LC_PAPER=C                 LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C      

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

other attached packages:
[1] mogene11stv1mmentrezgprobe_15.1.0 mogene11stv1mmentrezgcdf_15.1.0 
[3] AnnotationDbi_1.18.1              gcrma_2.28.0                    
[5] BiocInstaller_1.4.6               affy_1.34.0                     
[7] Biobase_2.16.0                    BiocGenerics_0.2.0              

loaded via a namespace (and not attached):
 [1] affyio_1.24.0         Biostrings_2.24.1     DBI_0.2-5           
 [4] IRanges_1.14.3        preprocessCore_1.18.0 RSQLite_0.11.1      
 [7] splines_2.15.0        stats4_2.15.0         tools_2.15.0        
[10] zlibbioc_1.2.0 

## END CODE ##