I’m analyzing one-color Agilent chips data (human 44k) with MeV (multiexperiment viewer). I’m trying to do the Gene Set Enrichment Analysis with MeV, so I need the annotation files. I therefore opened the Expression File Loader (Select filter loader/Other format files/Agilent files).
On Agilent website I found Human 44k Gene List file and Annotation file. When I try to load them on MeV it does not work. It blocks, and I’m forced to interrupt the loading. The same thing if I try to load the annotation file directly from the Expression File Loader panel.
Does anybody knows which are the proper annotation and feature extraction files I need to load into the Annotation panel and Agilent feature Extraction files panel respectively?
It has been a couple of years since I used TMeV, but when I last did, there was a limit on the number of probesets that could be imported for a dataset, definitely well below most chip sizes (~10k or so). They claimed was a limitation of Java (could increase somewhat by altering batch command line for memory allocation to 1024 rather than default of 512).
Hmm, are you sure that your array is supported by MeV? Have you looked here: ftp://occams.dfci.harvard.edu/pub/bio/MeV/annotation/bioconductor_2_6/supported_arrays.txt
If it's not on here it probably won't work with MeV. I only used MeV on Human Methylation 27 arrays
According to the MeV user manual, the annotation feature currently only works for Affymetrix data: http://www.tm4.org/mev_manual/Loading%20the%20Data.html#annotation-feature
Matthew, I'm not sure the probeset is that limited as the HumanMethylation27 chips I used have 27,000 probes.
Judy - my arrays were Illumina, and I think you can use the Agilent arrays
Try maRt: http://code.google.com/p/martool/
it works with single color Agilent arrays :)
Thank you vrey much to all of you for your help. In the meanwhile I understood that the annotation file has to be uploaded as a zip file.
Martin I'll try maRt as well, but I couldn't find a statistical analysis support there, or am I wrong?.
Rajesh, do you also have a link for gal files? I'm having problem in finding it...
thanks again
try Limma linear Model under the ArrayMenu. there is no tutorial at the moment, but it is pretty self explanatory.
I've trying to use Agilent txt microarray raw data with Mev and Mart unsuccessfully.
Eventually, I went using limma with R, and everything went OK.
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