I am contacting you because you are listed as the maintainer of the ArrayExpress Bioconductor ArrayExpress package. I tried to use the ArrayExpress function to access a large dataset stored in ArrayExpress: "E-GEOD-5258"
library("ArrayExpress") GEOD5258.batch <- ArrayExpress( "E-GEOD-5258" )
The function downloads all of the necessary files, but then exits with the following message:
ArrayExpress: Reading data files Loading required package: pd.u133aaofav2 Attempting to obtain 'pd.u133aaofav2' from BioConductor website. Checking to see if your internet connection works... Package 'pd.u133aaofav2' was not found in the BioConductor repository. The 'pdInfoBuilder' package can often be used in situations like this. Error in oligo::read.celfiles(filenames = file.path(path, unique(files))) : The annotation package, pd.u133aaofav2, could not be loaded. In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called ‘pd.u133aaofav2’ Error in readAEdata(path = path, files = dataFiles, dataCols = dataCols, : Unable to read cel files in/tmp/RtmpdN8fuF
The "E-GEOD-5258" dataset contains Affymetrix microarray data from two different array types: A-Affy-113 and A-Affy-33. The former is causing the problem, because its annotation cannot be found in Bioconductor under its original name. Instead, annotations for this microarray are available under the name "hthgu133a" .
I am not the only user who has run into this problem, see e.g.Help with error: 'pd.u133aaofav2 was not found in the BioConductor repository'.
ArrayExpress function does not have any arguments that would allow me to manually set the array annotation package. Perhaps that feature would be worth adding?
Many thanks in advance,