Hello all, I am new to bioconductor and I am running into a couple of problems converting a marrayNorm object to an exprSet object. I convert the marrayNorm object to an exprSet using the following: library("convert") xEset <- as(marrayNorm object, "exprSet") The problem is that there does not seem to be any probe level information in the exprSet i.e. > geneNames(monkey) NULL > featureNames(monkey) Error in featureNames(monkey) : no direct or inherited method for function 'featureNames' for this call This information is available in the marrayNorm object: > norm at maGnames@maInfo[1:10,] ID Name X22170 22170 DXF68S1E X21642 21642 ABCA2 X22209 22209 LOC56990 X22121 22121 PDZD2 X24284 24284 PACE X66999 66999 CD74 X110223 110223 DLD X110202 110202 EEF1A1 X21744 21744 GGA2 X22739 22739 FLJ14566 I can fix the gene names by doing the following geneNames(monkey) <- norm at maGnames@maInfo$Name but the same does not work with the feature names. Is the correct way to do this? Anyway round the feature name problem. Many thanks Daniel Brewer -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research

Hi Daniel -- Your work-around for adding geneNames to 'monkey' is the way to go -- here the problem is in the convert package, so perhaps the package maintainer will incorporate a fix. A featureNames method didn't exist for exprSet (it will in the next release), so for now geneNames is the way to access the information you want from an exprSet. Martin Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> writes: > Hello all, > > I am new to bioconductor and I am running into a couple of problems > converting a marrayNorm object to an exprSet object. I convert the > marrayNorm object to an exprSet using the following: > > library("convert") > xEset <- as(marrayNorm object, "exprSet") > > The problem is that there does not seem to be any probe level > information in the exprSet i.e. >> geneNames(monkey) > NULL >> featureNames(monkey) > Error in featureNames(monkey) : no direct or inherited method for > function 'featureNames' for this call > > This information is available in the marrayNorm object: >> norm at maGnames@maInfo[1:10,] > ID Name > X22170 22170 DXF68S1E > X21642 21642 ABCA2 > X22209 22209 LOC56990 > X22121 22121 PDZD2 > X24284 24284 PACE > X66999 66999 CD74 > X110223 110223 DLD > X110202 110202 EEF1A1 > X21744 21744 GGA2 > X22739 22739 FLJ14566 > > I can fix the gene names by doing the following > > geneNames(monkey) <- norm at maGnames@maInfo$Name > > but the same does not work with the feature names. Is the correct way > to do this? Anyway round the feature name problem. > > Many thanks > > Daniel Brewer > > -- > ************************************************************** > > Daniel Brewer, Ph.D. > > Institute of Cancer Research > > _______________________________________________ > 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

Daniel Brewer wrote: > Hello all, > > I am new to bioconductor and I am running into a couple of problems > converting a marrayNorm object to an exprSet object. I convert the > marrayNorm object to an exprSet using the following: > > library("convert") > xEset <- as(marrayNorm object, "exprSet") > > The problem is that there does not seem to be any probe level > information in the exprSet i.e. > >>geneNames(monkey) > > NULL > >>featureNames(monkey) > > Error in featureNames(monkey) : no direct or inherited method for > function 'featureNames' for this call > > This information is available in the marrayNorm object: > >>norm at maGnames@maInfo[1:10,] > > ID Name > X22170 22170 DXF68S1E > X21642 21642 ABCA2 > X22209 22209 LOC56990 > X22121 22121 PDZD2 > X24284 24284 PACE > X66999 66999 CD74 > X110223 110223 DLD > X110202 110202 EEF1A1 > X21744 21744 GGA2 > X22739 22739 FLJ14566 > > I can fix the gene names by doing the following > > geneNames(monkey) <- norm at maGnames@maInfo$Name > > but the same does not work with the feature names. Is the correct way > to do this? Anyway round the feature name problem. Hi, Daniel. Welcome to bioconductor. The geneNames slot of an exprSet is meant to hold the unique name for each feature on the array, like the affy probeset id, for example. It can hold the actual names of genes, but then will probably not be unique. In the larger picture, the exprSet is not meant to hold any annotation at all. It was designed to be used in conjunction with a bioconductor annotation package. I personally find exprSets a bit difficult to use when I am using my own annotation, just for this reason. What array platform are you using and what are you trying to accomplish with converting to an exprSet? Sean