Hi, I am trying to import a bunch of SMD files(64 files) which are from a single mocroarray chip. The following is what I did and what I got: 1. I started R in the directory that has all the .xls files 2. library("marray") 3. read.SMD("18195.xls"), returned: > read.SMD("18195.xls") Generating target sample info from all files Reading ... ./18195.xls An object of class "marrayRaw" @maRf [1] 2478 2705 6402 3182 10273 45691 more rows ... @maGf [1] 3891 4776 10829 5665 21048 45691 more rows ... @maRb [1] 356 342 351 351 348 45691 more rows ... @maGb [1] 235 256 252 255 242 45691 more rows ... @maW <0 x 0 matrix> @maLayout An object of class "marrayLayout" @maNgr [1] 12 @maNgc [1] 4 @maNsr [1] 32 @maNsc [1] 30 @maNspots [1] 46080 @maSub [1] TRUE TRUE TRUE TRUE TRUE 46075 more elements ... @maPlate factor(0) Levels: @maControls factor(0) Levels: @maNotes character(0) @maGnames An object of class "marrayInfo" @maLabels [1] "1" "2" "3" "4" "5" 45691 more elements ... @maInfo Name Clone.ID X13834 13834 IMAGE:342721 X13846 13846 IMAGE:233721 X13929 13929 IMAGE:50754 X13941 13941 IMAGE:126243 X14025 14025 IMAGE:234736 45691 more rows ... @maNotes [1] "" @maTargets An object of class "marrayInfo" @maLabels [1] "18195" @maInfo Experiment Cy3 Cy5 SlideName 1 BC91_minusTS_Bio-6_RNAeasy_1 Stratagene_aT BC-D-091_aT shbg054 @maNotes character(0) @maNotes [1] "" 4. read.SMD() (I tried to read all files), returned: > read.SMD() Generating target sample info from all files Reading ... ./18195.xls Reading ... ./19938.xls Error in "[<-"(`*tmp*`, , f, value = c(551, 167, 1617, 147, 2088, 153, : number of items to replace is not a multiple of replacement length > It seems that I can read in one file at a time (just like what I did read.SMD("18195.xls")), but I need to grab all the files together. Anyone has any idea? I am using R 2.2.0 on Linux. Thanks in advance! Kind regards, Zhuang Wu

If you are able to read one file at a time, but not as a collection, it may be that the arrays are from different print runs and the dimensions of the arrays are not be exactly the same. The last time I remember looking at this, the .xls header contains the printrun identifier. In addition, if you downloaded the experiment archive, it should contain information (i.e. .gal files) for each printrun used. Maybe look at the 18195 and 19938 arrays and determine if the layout is exactly the same. While not trival, a search of the BioC mailing list will give some options into combining data from different platforms into a single data set. I guess I would start with seeing if I could load a batches of files from the same print run and go from there. -kyle > From: "Wu, Zhuang" <zwu3 at="" partners.org=""> > Date: Mon, 9 Jan 2006 12:49:54 -0500 > To: <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] [marray] Importing SMD files into marray > > > Hi, I am trying to import a bunch of SMD files(64 files) which are from a > single > mocroarray chip. The following is what I did and what I got: > > 1. I started R in the directory that has all the .xls files > 2. library("marray") > 3. read.SMD("18195.xls"), returned: > >> read.SMD("18195.xls") > Generating target sample info from all files > Reading ... ./18195.xls > An object of class "marrayRaw" > @maRf > [1] 2478 2705 6402 3182 10273 > 45691 more rows ... > > @maGf > [1] 3891 4776 10829 5665 21048 > 45691 more rows ... > > @maRb > [1] 356 342 351 351 348 > 45691 more rows ... > > @maGb > [1] 235 256 252 255 242 > 45691 more rows ... > > @maW > <0 x 0 matrix> > > @maLayout > An object of class "marrayLayout" > @maNgr > [1] 12 > > @maNgc > [1] 4 > > @maNsr > [1] 32 > > @maNsc > [1] 30 > > @maNspots > [1] 46080 > > @maSub > [1] TRUE TRUE TRUE TRUE TRUE > 46075 more elements ... > > @maPlate > factor(0) > Levels: > > @maControls > factor(0) > Levels: > > @maNotes > character(0) > > > @maGnames > An object of class "marrayInfo" > @maLabels > [1] "1" "2" "3" "4" "5" > 45691 more elements ... > > @maInfo > Name Clone.ID > X13834 13834 IMAGE:342721 > X13846 13846 IMAGE:233721 > X13929 13929 IMAGE:50754 > X13941 13941 IMAGE:126243 > X14025 14025 IMAGE:234736 > 45691 more rows ... > > @maNotes > [1] "" > > > @maTargets > An object of class "marrayInfo" > @maLabels > [1] "18195" > > @maInfo > Experiment Cy3 Cy5 SlideName > 1 BC91_minusTS_Bio-6_RNAeasy_1 Stratagene_aT BC-D-091_aT shbg054 > > @maNotes > character(0) > > > @maNotes > [1] "" > > 4. read.SMD() (I tried to read all files), returned: > >> read.SMD() > Generating target sample info from all files > Reading ... ./18195.xls > Reading ... ./19938.xls > Error in "[<-"(`*tmp*`, , f, value = c(551, 167, 1617, 147, 2088, 153, : > number of items to replace is not a multiple of replacement length >> > > > It seems that I can read in one file at a time (just like what I did > read.SMD("18195.xls")), but I need to grab all the files together. Anyone has > any idea? I am using R 2.2.0 on Linux. Thanks in advance! > > Kind regards, > > Zhuang Wu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > This email message, including any attachments, is for the so...{{dropped}}