Hi, I am trying to analyze Mouse Exon 1.0 st array data using aroma.affymetrix and FIRMA model to find the splicing variants. CDF file : MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf ( downloaded from the aroma.affymetrix website) CEL files: 12 Mouse Exon 1.0 st arrays. ( 6 arrays for each strain A and B) and Within A and B, i have 3 arrays each of two experimental conditions)
1) I am not sure how the RMA normalization in aroma.affymetrix performs, is the normalization performed within array or between the array ? How do i pass arguments to the function to control the process of normalization ? 2) What are .js and .css files generated at the end of the analysis described in vignette ( Human Exon array ). Are there any third party software that could be used to analyze this out put ? 3) How do i convert the probe set ID or transcript ID into gene name ? Can i calculate the fold change in aroma.affymetrix ? Thank you, Sundar On Jul 27, 11:52 am, Sundar <sundar...@gmail.com> wrote: > 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 aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/