Hi, I am using two-colour spotted array data which I downloaded from the Stanford Microarray Database generated with GenePix 4000B. To read the data I use: RG<-read.maimages(files, source="genepix", path=".", columns=colList, fill=TRUE) colList is a list of name=value pairs, specifying the forground and background intensity columns for the two channels. This generates an error: Error in "[<-"(*tmp*, , i, value = NULL) : number of items to replace is not a multiple of replacement length. Thank you, Juerg Straubhaar [[alternative HTML version deleted]]

At 03:38 AM 30/07/2003, Straubhaar, Juerg wrote: >Hi, > >I am using two-colour spotted array data which I downloaded from the >Stanford Microarray Database generated with GenePix 4000B. To read the >data I use: > > RG<-read.maimages(files, source="genepix", path=".", columns=colList, >fill=TRUE) There is no reason why this command should not work if your inputs 'files' and 'colList' are specified correctly. Note however that source="genepix" has no meaning here. Data from the Stanford Microarray Database are in SMD rather than Genepix format, and 'source' is ignored anyway when 'columns' is specified. I would be prepared to give more help if you give the value of 'colList' and the first 50 lines of the first data file. Gordon >colList is a list of name=value pairs, specifying the forground and >background intensity columns for the two channels. > >This generates an error: > >Error in "[<-"(*tmp*, , i, value = NULL) : > > number of items to replace is not a multiple of replacement >length. > >Thank you, > >Juerg Straubhaar > > [[alternative HTML version deleted]] ---------------------------------------------------------------------- ----------------- Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Vic 3050, Australia Tel: (03) 9345 2326, Fax (03) 9347 0852, Email: smyth@wehi.edu.au, www: http://www.statsci.org

Dear Juerg, > Hi Gordon, > > The list colList has the value: > colList<-list(Gf="CH1I_MEAN", Gb="CH1B_MEAN", Rf="CH2I_MEAN", > Rg="CH2B_MEAN") > > The first 50 lines of the first data file are attached. Thanks for sending this information. You have a typo in your colList in that you should have Rb= instead of Rg=. If you correct that then the following command should work for you: RG <- read.maimages(files, columns=colList, check.names=FALSE, fill=TRUE) The main problem you had is that the SMD data file has column names with underline characters "_" which are normally converted by R into "." when the file is read into a data.frame. Therefore read.maimages has trouble finding the columns specified by colList. The column name conversion can be prevented by passing the argument check.names=FALSE to read.maimages. Another problem, which you had already recognized, is that the last column of the data file consists entirely of missing values, so fill=TRUE is required to make sure that the number of data columns agrees with the number of headings. Best wishes Gordon > Thank you very much for your help. > > Juerg Straubhaar, PhD > University of Massachusetts Medical School > > > -----Original Message----- > From: Gordon Smyth [mailto:smyth@wehi.edu.au] > Sent: Wednesday, July 30, 2003 6:33 AM > To: Straubhaar, Juerg > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] reading data into limma > > At 03:38 AM 30/07/2003, Straubhaar, Juerg wrote: >>Hi, >> >>I am using two-colour spotted array data which I downloaded from the >> Stanford Microarray Database generated with GenePix 4000B. To read the >> data I use: >> >> RG<-read.maimages(files, source="genepix", path=".", columns=colList, >>fill=TRUE) > > There is no reason why this command should not work if your inputs > 'files' > and 'colList' are specified correctly. Note however that > source="genepix" > has no meaning here. Data from the Stanford Microarray Database are in > SMD > rather than Genepix format, and 'source' is ignored anyway when > 'columns' > is specified. > > I would be prepared to give more help if you give the value of 'colList' > > and the first 50 lines of the first data file. > > Gordon > >>colList is a list of name=value pairs, specifying the forground and >> background intensity columns for the two channels. >> >>This generates an error: >> >>Error in "[<-"(*tmp*, , i, value = NULL) : >> >> number of items to replace is not a multiple of replacement >>length. >> >>Thank you, >> >>Juerg Straubhaar >> >> [[alternative HTML version deleted]] > > -------------------------------------------------------------------- ---- > --------------- > Dr Gordon K Smyth, Senior Research Scientist, Bioinformatics, > Walter and Eliza Hall Institute of Medical Research, > 1G Royal Parade, Parkville, Vic 3050, Australia > Tel: (03) 9345 2326, Fax (03) 9347 0852, > Email: smyth@wehi.edu.au, www: http://www.statsci.org