[BioC] frma and alternative CDFs

[Tine Casneuf [guest]]

Hi all,

I am trying to apply frma with an alternative Brainarray CDF to a microarray dataset. I cannot get this to work and found a relevant post on the bioC mailing list: http://article.gmane.org/gmane.science.biology.informatics.conductor/47887/match=frma+alternative+cdf 

I get the same error as mentioned on the post:

> test <- ReadAffy()
> test at cdfName <- "hgu133plus2hsentrezgcdf"
> library(frma)
>  test2 <- frma(test)
Error in rcModelWPLM(y = x1, w = w.tmp, row.effects = pe.tmp, input.scale = x4) : 
  row.effects should sum to zero
>  test2 <- frma(test, summarize = "random_effect")
Error in if (convi < 1e-04) break : missing value where TRUE/FALSE needed 


I get the same error with the most recent version of the brain array CDF (18.0.0). The suggested solution on the page mentioned above (brain array version 15 and hgu133afrmavecs version 1.2.0) dord not solve the problem for me.

Does anyone know which versions of the brainarray CDFs, and hgu133afrmavecs go together?

thanks a lot,

Tine

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.3 (2014-03-06)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

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

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

other attached packages:
[1] hgu133plus2frmavecs_1.2.0      frma_1.12.0                   
[3] hgu133plus2hsentrezgcdf_15.0.0 AnnotationDbi_1.22.6          
[5] affy_1.38.1                    Biobase_2.20.1                
[7] BiocGenerics_0.6.0            

loaded via a namespace (and not attached):
 [1] BiocInstaller_1.12.1  Biostrings_2.28.0     DBI_0.2-7            
 [4] GenomicRanges_1.12.5  IRanges_1.18.4        MASS_7.3-33          
 [7] RSQLite_0.11.4        affxparser_1.32.3     affyio_1.28.0        
[10] bit_1.1-12            codetools_0.2-8       ff_2.2-13            
[13] foreach_1.4.2         iterators_1.0.7       oligo_1.24.2         
[16] oligoClasses_1.22.0   preprocessCore_1.22.0 splines_3.0.3        
[19] stats4_3.0.3          tools_3.0.3           zlibbioc_1.6.0       


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