Hi, I'm new to microarray analysis with gene/exon type of arrays -in my case human gene 1.0 ST arrays. Now I have to analyze 9 such arrays (3 replicates for three conditions each) and I use the "low level" analysis as suggested in the corresponding vignette on aroma homepage
http://www.aroma-project.org/node/38 and subsequently some limma/affy code to get my "hot" genes list. In addition to this I looked at the CEL-files using Affymetrix Gene expression console and AltAnalyze, both using RMA-based method for gene summary. Besides the fact that I'm now left behind with 3 very different lists I would like to know whether the "low level" analysis does not exclude to look a little deeper into the underlying probesets that were used (or rejected) in order to summarize expression levels. I installed the package hugene10stprobeset.db, this should allow me to retrieve all relevant probesets for a given gene. Could I use this type of information to go back to my quantile normalized AffymetrixCelSet (csN) to retrieve the corresponding expression values for those probesets - or is this no way to go? On the long way I'd like to write a little exporter that allows the per probeset extraction of the data in a form that allows to be displayed in genome browser (like the affy exon panel on UCSC)-> something like a bed or gff file. Another question related to the same dataset: what type of filtering is suggested in order to find a cut-off that might allow the differentiation between expressed and non-expressed genes. With the procedure as pointed out above using Aroma I get 23000 genes - most likely not all of them are really expressed! Unfortunately the vast amount of genes is no good for the p-value correction, basically no genes survive this step with p-values lower than 0.1. I'd be glad for any type of suggestion which direction I might have to go! Maxim -- 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/
