Hi, Is it possible to convert GSE obtained using getGEO() into an MAList? I tried > gse = getGEO("GSE17308") > ma = GDS2MA(gse) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "Meta", for signature "list" GSE is not the same as GDS, so it's not surprising that it isn't working. However, I don't understand how GSE should be different from GDS to arrive to the same data structure. What I ultimately want is to able to connect to limma analysis, which in the examples uses an MAList. Any help would be appreciated, thank you. :) Timothy [[alternative HTML version deleted]]

Hi Timothy, you can run limma for differential expression analysis on your object 'gse' which is a list of ExpressionSets, which contains one single element because the dataset is not too large. This contains normalized log2 ratios after pre-processing done by the authors. If you want to do quality control and/or apply your own pre-processing you can because the authors of this particular GSE have also provided the raw data (scanner output txt files). To download these files you can use the GEOquery function getGEOSuppFiles. After the download has completed you will need to import the data using functions provided in limma, see Section 4 in the limmaUsersGuide(). HTH, James. On 05/19/2010 01:13 PM, Timothy Wu wrote: > Hi, > > Is it possible to convert GSE obtained using getGEO() into an MAList? > > I tried > >> gse = getGEO("GSE17308") >> ma = GDS2MA(gse) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "Meta", for signature > "list" > > GSE is not the same as GDS, so it's not surprising that it isn't working. > However, I don't understand how GSE should be different from GDS to arrive > to the same data structure. What I ultimately want is to able to connect to > limma analysis, which in the examples uses an MAList. Any help would be > appreciated, thank you. :) > > Timothy > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >