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I have a file created using the Expresion Console of Affymetrix. The file contains lines :
Probe Set ID GSM154768.ex2.mas5-Signal GSM154768.ex2.mas5-Detection GSM154768.ex2.mas5-Detection p-value GSM154769.ex2.mas5-Signal……..
AFFX-BioB-5_at 298.9997 P 0.004017214 290.1384 P……..
So, this corresponds quite well to the description in the MeV manual. I tried to load it using the loader menu option for "Affymetrix GCOS(using MAS5)Files", of course with "Intensity with Detetction and P-values" checked. But in the pop-up box the top bar remains empty and the bottom bar goes to 99% and then it stalls. I thought that the problem was maybe with the loading of the annotation file. I tried as well to uncheck "load annotation" as downloading automatically as using a local file. When I use a local file a list of names appears in the DOS box of Windows, so something is happening. However the loading still stalls the same way, so the problem might be with the Affymatrix expression data file although it looks good.
Did someone already successfully transfer date from Expression Console to MeV ? Any clue about what I am missing ?
University of Brussels
Well, in the mean time I discovered myself the solution : it turns out that the files created by the Affymetrix expression Console contain at the end a few extra end-of-line characters. These make MeV stall and the cure is to use an editor to remove them….
Hi there Guy,
I'm glad to hear you've already figured out the problem with the Affy files. Would you mind doing me a favor and sending me an example of one of these files with the extra end-of-line characters? It doesn't need to be real data, but it would help us fix the file loader if we had a known problem-causing file to test with.
Dear Eleanor, I just looked back at the forum and saw your question. But I have a (silly) problem : I have not yet figured out how I can send a file as attachment in the forum mail system…