I've been trying to use FIRMA analysis (http://www.aroma-project.org/vignettes/FIRMA-HumanExonArrayAnalysis) on my mouse arrays ( Mouse Exon 1.0 ST Array - http://aroma-project.org/chipTypes/MoEx-1_0-st-v1).
It looks like the scripts have completed successfully, but I have a few questions: 1) How can I figure out which genes/exons correspond with the "unitName" and "groupName" fields returned by "extractDataFrame(fs, addNames=TRUE)"? http://www.aroma-project.org/vignettes/UsingGenomeGraphsWithFIRMA implies that I can download a "NetAffx tabular text files" from Ayymetrix and use that. However, I cannot get Affymetrix to provide me with a login to get that file. I hoped that I could load ‘MoEx-1_0-st-v1,HB20100926.acs’ and use that to get enough probe information to reconstruct the names using annmap, but I cannot figure out how to load the .acs file. 2) How do I run FIRMA after I change the tags? I switch from 'MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf' to 'MoEx-1_0-st-v1,U-Ensembl50,G-Affy,EP.cdf' in the hope that the Ensemble file would have easier to interpret names. However, after rerunning my analysis script, it looks like aroma is reading things from intermediate files. I get the error message: *Error: Cannot set CDF. The specified CDF structure ('MoEx-1_0-st-v1,U-Ensembl50,G-Affy,EP,monocell') is not compatible with the chip type ('MoEx-1_0-st-v1,coreR1,A20080718,MR,monocell') of the CEL file. The number of cells do not match: 279841 != 224202* I know that FIRMA dumps many intermediate files, but I would prefer not to delete things at random in the hope that something will eventually work. 3) How can I update the .cdf files? I would like to use the brainarray .cdf files (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp) because they are regularly updated. However, (based on the results of the FIRMA run) their .cdf files do not have the correct exon/gene annotations. I can figure out which exons should be paired with which genes from annmap, but I cannot figure out how to store this information in the .cdf file. Thank you, -Sam -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
