Hi, I’ve just started learning Bioconductor. I downloaded the data lc7b048rex2.DAT from http://llmpp.nih.gov/lymphoma/ . When I tried to view the special homogenueity of hybridization, this was the error I’ve got: >x=read.delim(“lc7b048rex2.DAT”) bg1<- spatialLayout(value=x$CH1B, >row=x$ROW, col=x$COL, block=x$GRID) Error in if (totalNumberOfValues%%(max(col) * nrOfBlocksPerRow) != 0) { : missing value where TRUE/FALSE needed Then I got rid of the text information in the first 7 rows >xx<-x[8:9223,] >bg2<- spatialLayout(value=xx$CH1B, row=xx$ROW, col=xx$COL, block=xx$GRID) Warning messages: 1: "-" not meaningful for factors in: Ops.factor(block, 1) 2: "-" not meaningful for factors in: Ops.factor(block, 1) I had the same error massage even when I specified nrOfBlocksPerRow as 1 or 8 instead of the default value of 4. Every tuple of bg2 now has a value of “NA”. Of course, I cannot plot bg2 using plot.imageMatrix( ). How can I get the spatial layout of the background? Any help is greatly appreciated. Many thanks. Irene Married. http://lifeevents.msn.com/category.aspx?cid=married

Hi Irene, if you use the following lines it should work. x <- read.delim(file="lc7b048rex2.DAT", skip=8, header=FALSE) xHeader<- scan(file="lc7b048rex2.DAT", nlines=1, what="character", sep="\t") colnames(x) <- xHeader library(arrayMagic) bg1<- spatialLayout(value=x$CH1B, row=x$ROW, col=x$COL, block=x$GRID) plot.imageMatrix(bg1) Your subsetting operation xx<-x[8:9223,] does have a different effect; e.g. try: str(xx) Nevertheless I have not been aware that I always used already processed ScanAlyze files, such that the example in arrayMagic does not work with the original data files. I will clarify this. Best Regards Andreas Irene Li wrote: > Hi, > > I?ve just started learning Bioconductor. I downloaded the data > lc7b048rex2.DAT from http://llmpp.nih.gov/lymphoma/ . When I tried to > view the special homogenueity of hybridization, this was the error I?ve > got: > >> x=read.delim(?lc7b048rex2.DAT?) bg1<- spatialLayout(value=x$CH1B, >> row=x$ROW, col=x$COL, block=x$GRID) > > Error in if (totalNumberOfValues%%(max(col) * nrOfBlocksPerRow) != 0) { : > missing value where TRUE/FALSE needed > > Then I got rid of the text information in the first 7 rows > >> xx<-x[8:9223,] >> bg2<- spatialLayout(value=xx$CH1B, row=xx$ROW, col=xx$COL, block=xx$GRID) > > Warning messages: > 1: "-" not meaningful for factors in: Ops.factor(block, 1) > 2: "-" not meaningful for factors in: Ops.factor(block, 1) > > I had the same error massage even when I specified nrOfBlocksPerRow as 1 > or 8 instead of the default value of 4. Every tuple of bg2 now has a > value of ?NA?. Of course, I cannot plot bg2 using plot.imageMatrix(?). > > How can I get the spatial layout of the background? > > Any help is greatly appreciated. > > Many thanks. > > Irene > > > Married. http://lifeevents.msn.com/category.aspx?cid=married > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconducto > r