Hi, I am new to the Exon array concept. I am trying to analyze Mouse Exon 1.0 st array data using aroma.affymetrix and FIRMA model. Few questions i have are below.
1) To get a start i have just implemented the code described in vignette "FIRMA: Human exon array analysis. " There are certain .CEL files and other extension files generated. How can i read them into R ? How do i know what information they carry ? Is there any other software i can upload them to read these files ? How do i get control of the analysis in applying extractMatrix() or extractDataFrame() , readUnits() functions ? 2) I am unable to get a clear understanding of what the background calculation are taking place using the functions ( used to generate the files in Q.1) ? Except that these function performs QC, Normalization, Summarization etc. I am lacing clear understanding how those methods are implemented on Exon arrays , when compared to 3' prime arrays ? for instance,, In 3'-IVT arrays, I have the control of Normalizing within the group or across the group, where as in this exon array analysis I'm not sure what the function does ? 3) I am not sure what other applications i can use with the end result of summarization / FIRMA. can i get a list of differentially expressed genes ? splicing variant list ? upload the list of genes into pathway studio for further analysis ? What methods should i use ? can i use similar statistics that i use for 3' IVT arrays ? ( t-test, Bonferroni etc. ?) Please enlighten me a bit on this exon array analysis Thank you, Sundar -- 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 firstname.lastname@example.org To unsubscribe and other options, go to http://www.aroma-project.org/forum/