I'm analyzing >30 Affymetrix miRNA 4.0 microarrays. As the corresponding miRNA 4.0 CDF is not available from BioC, I downloaded it from the Affymetrix website. I then created a CDF environment using make.cdf.env (makecdfenv package) and read in the data as:
rawData <- ReadAffy( ) rawData@cdfName <- 'mirna40'
The returned AffyBatch object seems perfectly fine to me. It has meaningful row.names and runs smoothly through rma (affy).
However, I would like to perform extensive QC for these data before proceding with differential expression analysis. To this end, I understand that the QCReport (affyQCReport package) and/or the qc (simpleaffy) functions are valuable options. Unfortunately, a call to either function currently raises the error below:
QCReport( rawData, file = 'QC.pdf' ) Error in ans[[i]][, i.probes] : subscript out of bounds qc( rawData ) Error in ans[[i]][, i.probes] : subscript out of bounds
Debugging suggests that the error is generated by the signalDist function, but I was unable to go further.
I would really appreciate your help on this. Thanks a lot in advance.
sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-unknown-linux-gnu (64-bit) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8  LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  hgu95av2cdf_2.15.0 affydata_1.13.1 affyQCReport_1.44.0  lattice_0.20-29 BiocInstaller_1.16.1 makecdfenv_1.42.0  affyio_1.34.0 simpleaffy_2.42.0 gcrma_2.38.0  genefilter_1.48.1 affy_1.44.0 Biobase_2.26.0  BiocGenerics_0.12.1 loaded via a namespace (and not attached):  affyPLM_1.42.0 annotate_1.44.0 AnnotationDbi_1.28.1  Biostrings_2.34.1 DBI_0.3.1 GenomeInfoDb_1.2.4  grid_3.1.2 IRanges_2.0.1 preprocessCore_1.28.0  RColorBrewer_1.1-2 RSQLite_1.0.0 S4Vectors_0.4.0  splines_3.1.2 stats4_3.1.2 survival_2.37-7  tools_3.1.2 XML_3.98-1.1 xtable_1.7-4  XVector_0.6.0 zlibbioc_1.12.0