I was wondering, if it is possible/advised to use the fRMA algorithm to also analyse HT_MG-430_PM arrays.
The Affymetrix website states that: "The GeneChip HT MG-430 PM Array Plate enables high-throughput expression profiling of 16, 24, or 96 samples at a time using the same industry-standard content as the GeneChip Mouse Genome 430 2.0 Array".
Hence I hope, that I can still apply the fRMA algorithm also to this type of array. However if I read in the AffyBatch in a regular manner and just provide the input.vecs to fRMA, I end up with this type of error:
#library("mouse4302frmavecs") #data(mouse4302frmavecs) myEset <- frma(myAffyBatch,input.vecs = mouse4302frmavecs) Error in frmaAffyBatch(object, background, normalize, summarize, input.vecs, : Mismatch between pmindex(object) and names of input.vecs and unable to create unique mapping.
It turns out, that the probe names do not match:
 "1415670_PM_at" "1415671_PM_at" "1415672_PM_at"
 "1415670_at" "1415671_at" "1415672_at"
The initial approach, which I considered was a little gsub manimulation of the names, but I have doubts to mess with the probe assignments too much and end up with wrongly normalized expression calls, since also the length of the vectors does not match (difference of 40 probes).
Since the ReadAffy function offers a possibility to modify the cdfname, I rather tested this (unsuccessful) approach:
myAffyBatch <- ReadAffy(celfile.path="./data/CELfiles/", cdfname="mouse4302")
myEset <- frma(myAffyBatch,input.vecs = mouse4302frmavecs)
Error in exprs(object)[index, , drop = FALSE] : subscript out of bounds In addition: Warning messages: 1: replacing previous import by ‘utils::tail’ when loading ‘mouse4302cdf’ 2: replacing previous import by ‘utils::head’ when loading ‘mouse4302cdf’
So I would kindly ask for help, if and how I can reasonably analyse HT_MG-430_PM Arrays with fRMA.
Thanks a lot
> sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale:  LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252  LC_MONETARY=German_Germany.1252 LC_NUMERIC=C  LC_TIME=German_Germany.1252 attached base packages:  parallel stats graphics grDevices utils datasets methods base other attached packages:  htmg430pmcdf_2.18.0 mouse4302cdf_2.18.0 mouse4302frmavecs_1.5.0  mouse430a2frmavecs_1.3.0 frma_1.22.0 limma_3.26.5  affy_1.48.0 Biobase_2.30.0 BiocGenerics_0.16.1  BiocInstaller_1.20.1 loaded via a namespace (and not attached):  AnnotationDbi_1.32.3 affxparser_1.42.0 XVector_0.10.0  splines_3.2.3 GenomicRanges_1.22.3 zlibbioc_1.16.0  MASS_7.3-45 IRanges_2.4.6 bit_1.1-12  foreach_1.4.3 GenomeInfoDb_1.6.1 tools_3.2.3  SummarizedExperiment_1.0.2 ff_2.2-13 DBI_0.3.1  iterators_1.0.8 oligoClasses_1.32.0 preprocessCore_1.32.0  oligo_1.34.2 affyio_1.40.0 S4Vectors_0.8.7  codetools_0.2-14 RSQLite_1.0.0 Biostrings_2.38.3  stats4_3.2.3