DeaR bioconductors, I am trying to process results for some Illumina datasets obtained from GEO repository (with geoquery). Usually signals from illumina arrays are filtered using detection score p-value. I can see that these score values are available on the GEO webpage, however I do not know where (if it all) these values are stored in the ExpressionSets obtained with the getGEO function. Any help on this or advice on alternatives to filter illumina data with detection scores are appreciated in advance! Have a nice day, Ale? Maver Ales.Maver at gmail.com

Hi Ales, suppose that the ExpressionSet returned by GEOquery is called eset, then dims(eset) will return the dimensions of all the members of the assayData of eset, which will contain exprs (default) and then maybe some other matrices say exprs.se which you can access with assayData(eset)$exprs.se (if that is indeed the name of the matrix). HTH, J. Ale? Maver wrote: > DeaR bioconductors, > I am trying to process results for some Illumina datasets obtained > from GEO repository (with geoquery). Usually signals from illumina > arrays are filtered using detection score p-value. I can see that > these score values are available on the GEO webpage, however I do not > know where (if it all) these values are stored in the ExpressionSets > obtained with the getGEO function. > Any help on this or advice on alternatives to filter illumina data > with detection scores are appreciated in advance! > > Have a nice day, > > Ale? Maver > Ales.Maver at gmail.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

On Sun, Jul 26, 2009 at 7:55 AM, Aleš Maver <ales.maver@gmail.com> wrote: > DeaR bioconductors, > I am trying to process results for some Illumina datasets obtained > from GEO repository (with geoquery). Usually signals from illumina > arrays are filtered using detection score p-value. I can see that > these score values are available on the GEO webpage, however I do not > know where (if it all) these values are stored in the ExpressionSets > obtained with the getGEO function. > Any help on this or advice on alternatives to filter illumina data > with detection scores are appreciated in advance! > Hi, Ales. The ExpressionSet will not have the p-values for detection included unless you use getGEO with the parameter GSEMatrix=FALSE and then construct the ExpressionSet yourself. There is an example of doing so in the vignette, but you will need to change the details to match the situation at hand. If there is raw data available for your dataset, you could try using that instead (with lumi or beadarray packages, as an example) and combine it with the phenodata from the downloaded ExpressionSet. Sean [[alternative HTML version deleted]]