Hi all, I am using aroma.affymetrix for an analysis on Human Exon Array data and would need to access the individual probe intensities mapped to probe_id after background correction and normalization. Is there an easy way to do this? Below you can see what I have tried so far.
With the notation on http://www.aroma-project.org/node/37 I am looking at object csN - data at probe-level after BC and QN > affyBatch <- extractAffyBatch(csN) # I get an error message about package "huex10stv2cdf" not being available from Bioconductor. > probes_matrix <- extractMatrix(csN, cells=NULL, field=c("intensities", > "stdvs", "pixels"), drop=FALSE, verbose=verbose) # I do not get any > information about which probe the intensity belongs to > intensities <- getIntensities(csN) # no probe or array information > unitIntensities <- getUnitIntensities(csN, verbose=verbose) # I get transcript and probeset information and the individual intensities of the 4 probes in each probeset, but numbered 1 to 4, so I still cannot map them to their target sequence. I have now run out of ideas so I would really appreciate any suggestions. Thank you very much in advance for your help. Best regards, Maria Rodrigo PhD student in Biostatistics Department of Haematology, Medical Center Aalborg Hospital Science and Innovation Center AHSIC Denmark -- 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/
