Hi folks,
I am currently running affy to process some microarray data and got some error message when I called mas5
> cel = ReadAffy(cdfname="hgu133ahsentrezgcdf")
> e = exprs(mas5(cel))
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...Error in .validate_assayDataElementReplace(obj, value) :
object and replacement value have different dimensions
I have googled around but couldn't fix it.
I also include the sessionInfo below. Thanks so mucn for your hel!
sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BiocInstaller_1.30.0 hgu133ahsentrezg.db_18.0.0
[3] org.Hs.eg.db_3.6.0 hgu133ahsentrezgcdf_18.0.0
[5] affy_1.58.0 preprocessCore_1.42.0
[7] annotate_1.58.0 XML_3.98-1.11
[9] AnnotationDbi_1.42.1 IRanges_2.14.10
[11] S4Vectors_0.18.2 Biobase_2.40.0
[13] BiocGenerics_0.26.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 zlibbioc_1.26.0 bit_1.1-13 xtable_1.8-2
[5] blob_1.1.1 tools_3.5.0 DBI_1.0.0 bit64_0.9-7
[9] digest_0.6.15 affyio_1.50.0 bitops_1.0-6 RCurl_1.95-4.10
[13] memoise_1.1.0 RSQLite_2.1.1 compiler_3.5.0 pkgconfig_2.0.1
It's working fine for me using some similar old (1st generation) mouse arrays that I had at hand.
However, I noticed that you are using version 18 of the custom CDF, which was released more than 4 years ago.... Maybe these old CDFs are not compatible anymore with the current version of R/BioC? The latest custom CDFs have version 22.
> affy.data <- ReadAffy(cdfname="moe430ammentrezg") > head(exprs(mas5(affy.data))) background correction: mas PM/MM correction : mas expression values: mas background correcting...done. 12487 ids to be processed | | |####################| KOcontrol2.CEL KOcontrol3.CEL KOcontrol5.CEL KOWY7.CEL KOWY8.CEL 100017_at 281.03718 300.30893 349.325229 492.731476 368.46865 100019_at 108.10902 155.00969 39.096128 168.429747 137.63542 100037258_at 364.01194 366.23043 377.799635 406.224641 422.37511 100038347_at 570.81180 561.18303 368.534263 409.663796 479.11048 100038746_at 12.95754 20.76136 5.290644 3.778448 2.74952 100040018_at 233.81823 308.00518 225.531818 326.181424 382.40645Thanks for your help. I used another computer for the same code, and it worked. It is weird that it just didn't work on my Mac.