I have been trying to create a package with annotation data for GeneChip miRNA 4.0 Array. Affymetrix people provided me with miRNA-4_0-st-v1.cdf and I created a annotation package using makecdfenv and affxparser. Using this package, I was able to read CEL files correctly, but then no subsequent processing is possible, as some data seems to be missing. Below I show one example for the error message I get. Do you have any idea, what needs to be done here? I couldn't find information in respective vignettes.
library(makecdfenv) library(affxparser) convertCdf("miRNA-4_0-st-v1.cdf", "mirna40cdf", version=4, verbose=TRUE) pkgpath <- tempdir() make.cdf.package("mirna40cdf", version = packageDescription("makecdfenv", field = "Version"), species="", unlink=TRUE, compress=FALSE, package.path = pkgpath)
##package installation from DOS shell (R CMD INSTALL "path to package") library(mirna40cdf)library(affy)
myData = ReadAffy()
AffyBatch object size of arrays=541x541 features (18 kb) cdf=miRNA-4_0 (36249 affyids) number of samples=4 number of genes=36249 annotation=mirna40 notes=
myQC = qc(myData)
Error in setQCEnvironment(cdfn) : Could not find array definition file ' mirna40cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually.