Dear Group, I have been trying to create rawset using ArrayExpress for the following array dataset. I have error when I ran the following. Any suggestion
First error i got as " Error in smartReadCEL(filenames, sampleNames, headdetails = headdetails) : End of file reached unexpectedly. Perhaps this file is truncated. "
rawset= ArrayExpress("E-MTAB-6877") trying URL 'https://www.ebi.ac.uk/arrayexpress/files/A-GEOD-16686/A-GEOD-16686.adf.txt' Content type 'text/plain' length 686970 bytes (670 KB) downloaded 670 KB
trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-6877/E-MTAB-6877.sdrf.txt' Content type 'text/plain' length 34358 bytes (33 KB) downloaded 33 KB
trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-6877/E-MTAB-6877.idf.txt' Content type 'text/plain' length 3944 bytes downloaded 3944 bytes
Copying raw data files
trying URL 'https://www.ebi.ac.uk/arrayexpress/files/E-MTAB-6877/E-MTAB-6877.raw.1.zip' Content type 'application/zip' length 54983 bytes (53 KB) downloaded 53 KB
Unpacking data files ArrayExpress: Reading pheno data from SDRF ArrayExpress: Reading data files Platform design info loaded. Reading in : C:\Users\32493\AppData\Local\Temp\Rtmpsxphr1/DJN084HuGene2.CEL Error in smartReadCEL(filenames, sampleNames, headdetails = headdetails) : End of file reached unexpectedly. Perhaps this file is truncated.
Error in readAEdata(path = path, files = dataFiles, dataCols = dataCols, : Unable to read cel files inC:\Users\32493\AppData\Local\Temp\Rtmpsxphr1 Error in ae2bioc(mageFiles = expFiles, dataCols = dataCols, drop = drop) : ArrayExpress: Unable to read assay data