[aroma.affymetrix] Error when analyzing CEL files using process() function: "No permission to modify existing file: /probeData..."

Hi Henrik: I just come across an unusual error when using aroma.affymetrix on our high-memory HPC machine. It may or may not be platform-specific, and I'll give you all the information I can in the hopes of isolating and identifying the error. Traceback: > traceback() 18: stop(cond) 17: thr

Re: [aroma.affymetrix] Error when analyzing CEL files using process() function: "No permission to modify existing file: /probeData..."

Hi, interesting. A quick guess is that the input file, i.e. rawData/NIK_2014/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL is write protected (e.g. file owned by someone else). This could be the reason, because internally that file is copied and used as a template and the copy may inherit the fi

Re: [aroma.affymetrix] Error when analyzing CEL files using process() function: "No permission to modify existing file: /probeData..."

Hi Henrik: Thank you for the prompt reply. You are right- the .CEL files are all read only (see their permissions, below) rtraborn@Mason: /N/dc2/scratch/rtraborn/ML_Project/NIK_2014/rawData/NIK_2014/HuEx-1_0-st-v2> ls -lkhtra -r--r--r-- 1 ... 63M Jan 25 2011 GSM709338_HSB194-VFC-R.CEL -r--

Re: [aroma.affymetrix] Error when analyzing CEL files using process() function: "No permission to modify existing file: /probeData..."

Hi, good that it works for you with this workaround. The fix in aroma is fairly simple(*). I'll let you know when an updated version is available. (*) DETAILS: This has to do with base::file.copy() and its argument 'copy.mode' which was introduced in R 2.13.0 (April 2011). The thing is that th