Hi everyones, I have two different datasets of cDNA microarray experiments regarding the same kind of samples, but two different kind of slices, in the sense that dataset1 was hybridized with slides with set of genes, and dataset2 was hybridized with slides with set of the sames genes(so ... clone phisical identity) PLUS other genes. So now I would like to merge the results from the two(of course only,for the common genes). My idea was 1) load each dataset alone and normalize it (I am using limma) That's OK 2) merge the 2 datasets with MergeMaid. That's NOT OK because first of all MergeMaid need ExprSet class object in input, and using as(RG,"ExprSet") function from Biobase create ExprSet2 class object. Second because in this way I can import only RG class object and not MA class object, but I suppose I HAVE to normailzed each dataset on its own! So could anyone help me? Maybe, I miss the right way to use MargeMaid... Or anyway there is another methods the better marge datasets with common genes? Thank you,everyone! Silvano Silvano Piazza LNCIB Trieste, Area Science Park

If you know that your slides have the same clones/probes and the reference, etc. is the same, you could directly combine the RG objects. You just need to have the "rows" from the RG objects matching up. So, if you have a unique id in the genes slot of the RG object, you could use the smaller group to get only those genes from the larger doing something like: RG.larger2smaller <- RG.larger[as.character(RG.larger$genes$uniqueid) %in% as.character(RG.smaller$genes$uniqueid),] The idea here is that for all genes where the unique ID in the larger set is in the smaller set, keep that gene. Otherwise, that gene will not be kept. RG.larger2smaller will have then have the same number of genes as the RG.smaller. Then, you will have to make sure they are ordered in the same way. Sean On Oct 28, 2004, at 12:22 PM, Silvano Piazza wrote: > Hi everyones, > > I have two different datasets of cDNA microarray experiments regarding > the same kind of samples, but two different kind of slices, in the > sense that dataset1 was hybridized with slides with set of genes, and > dataset2 was hybridized with slides with set of the sames genes(so ... > clone phisical identity) PLUS other genes. > > So now I would like to merge the results from the two(of course > only,for the common genes). My idea was > 1) load each dataset alone and normalize it (I am using limma) > That's OK > 2) merge the 2 datasets with MergeMaid. > That's NOT OK because first of all MergeMaid need ExprSet class > object in input, and using as(RG,"ExprSet") function from Biobase > create ExprSet2 class object. > Second because in this way I can import only RG class object and not > MA class object, but I suppose I HAVE to normailzed each dataset on > its own! > > So could anyone help me? > Maybe, I miss the right way to use MargeMaid... > > Or anyway there is another methods the better marge datasets with > common genes? > > Thank you,everyone! > > Silvano > > > Silvano Piazza > LNCIB Trieste, > Area Science Park > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

Have you tried using the merge() command in limma, which is provided for just this purpose? Where are your gene IDs stored? If they are in MA$genes$ID, then you can normalize your two data sets to get MA1 and MA2, and then simply MAmerged <- merge(MA1, MA2) If your IDs are not in MA$genes$ID, then set rownames(MA1$M) and rownames(MA2$M) to be your gene IDs. Gordon >Date: Thu, 28 Oct 2004 18:22:11 +0200 >From: Silvano Piazza <piazza@lncib.it> >Subject: [BioC] Merging different datasets? >To: bioconductor@stat.math.ethz.ch >Message-ID: <41811CB3.3010506@lncib.it> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > >Hi everyones, > >I have two different datasets of cDNA microarray experiments regarding >the same kind of samples, but two different kind of slices, in the sense >that dataset1 was hybridized with slides with set of genes, and >dataset2 was hybridized with slides with set of the sames genes(so ... >clone phisical identity) PLUS other genes. > >So now I would like to merge the results from the two(of course only,for >the common genes). My idea was >1) load each dataset alone and normalize it (I am using limma) > That's OK >2) merge the 2 datasets with MergeMaid. > That's NOT OK because first of all MergeMaid need ExprSet class >object in input, and using as(RG,"ExprSet") function from Biobase >create ExprSet2 class object. >Second because in this way I can import only RG class object and not MA >class object, but I suppose I HAVE to normailzed each dataset on its own! > >So could anyone help me? >Maybe, I miss the right way to use MargeMaid... > >Or anyway there is another methods the better marge datasets with common >genes? > >Thank you,everyone! > >Silvano > > >Silvano Piazza >LNCIB Trieste, >Area Science Park