Hi Jiang. Its helpful to use meaningful subject headers, so that others can search the mailing lists. So, I've changed your messages to a new thread. Comments below.
> Hi, > I have a question can you help me. That's about using FIRMA. I > cannot get the result after I run FIRMA. I only found the score.CEL > files but they cannot be opened. So may you give me some suggestion? > Thanks very much. > Best, > Jiang You shouldn't need to deal directly with the CEL files. You can access the FIRMA scores by using extractDataFrame(). For example: [...] firma <- FirmaModel(plm) fit(firma, verbose=verbose) fs <- getFirmaScores(firma) fsDf <- extractDataFrame(fs) The 'fsDf' should be a data.frame object containing the FIRMA scores, assuming you've run all the previous steps mentioned in the vignette: http://groups.google.com/group/aroma-affymetrix/web/human-exon-array-analysis > Hi, > When I run FIRMA, I got the FIRMAscores.CEL files, but I cannot open > it > using TXT. They are binary files, but as mentioned above, you shouldn't need to deal with them directly. > So how I can check my result of the FIRMA. The result > folder is > empty. Another, if I want to add the samples& groups info to the exon > array, > what is the format of it? I wirte like this: > sample1 group1 > sample2 group1 > sample3 group2 > sample4 group3 > and put it in the ..\annotationData\samples\, that's right? > Thanks, > Jiang > FIRMA is a single sample method, in the sense that it doesn't need replicates. Therefore, it does not need this information. Cheers, Mark ------------------------------ Mark Robinson, PhD (Melb) Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ -- 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en
