I have several Clariom D Human Arrays (Affymetrix) for which I want to remove some probes (the same set of probes in all of them).
I thought it might be possible to construct a library package in R with pdInfoBuilder. In order to do this, I downloaded the Analysis r1 files from Affy website and I filtered out the set of probes from the .pgf and .clf files. Then I created the library using the clf, pgf, mps and annotation (probeset and transcript) files. However, when I read my arrays (CEL files) with oligo package (Bioconductor), I still observe signal for the probes I removed. How can it be possible?
Is there any oher way to exclude such probes? EDIT:
I carried out the next steps:
To make the new library:
library(pdInfoBuilder) pkg <- new("AffyHTAPDInfoPkgSeed", pgfFile = pgfFile, clfFile = clfFile, probeFile = csvProbAnno, transFile = csvTransAnno, coreMps = coreMpsFile, extendedMps = extendedMpsFile, fullMps = fullMpsFile, biocViews = "AnnotationData", genomebuild = "hg38", organism = "Human", species = "Homo sapiens", url = "", chipName = 'clariom.d.human') makePdInfoPackage(pkg, destDir=".")
Then I compressed (.tar.gz) the directory where the new package is located and installed it with:
To read the CEL files:
library(oligo) library(pd.clariom.d.human) raw_data <- read.celfiles(list.celfiles())