Hi, I tried to use imageplot to see my normalized data in limma package, I tried both command as following, > imageplot(log2(RB$Rb[,1]),RB$printer,low="white",high="red") and > imageplot(MA$M[,1],RB$printer,zlim=c(-3,3)) and >imageplot(MA$M[,1],layout=list(ngrid.r=12,ngrid.c=4,nspot.r=21,nspot. c=21)) they all gave me the same kind of error messages: Error in imageplot(log2(RB$Rb[, 1]), RB$printer, low = "white", high = "red") : Number of image spots does not agree with layout dimensions Or Error in imageplot(MA$M[, 1], RB$printer) : Number of image spots does not agree with layout dimensions Any idea is greatly appreciated! Thanks ******************************** Joyce Gu M.S. Scientific Programmer Cancer Genomics Group Baylor College of Medicine Phone: 832-824-4680 Fax: 832-825-4038

Hi Joyce, As the error message suggests, the number of spots in your RB/MA object and the layout you have specified don't agree. Try dim(RB$Rb) dim(MA$M) to determine how many spots (rows) and arrays (columns) you have read in and converted to log-ratios. Does the number of spots returned agree with the number you have specified in the layout arguments of imageplot() (12*4*21*21 = 21168)? If not then you need to correct this so that the two agree. Best wishes, Matt Ritchie > Hi, > I tried to use imageplot to see my normalized data in limma package, I > tried both command as following, >> imageplot(log2(RB$Rb[,1]),RB$printer,low="white",high="red") > and >> imageplot(MA$M[,1],RB$printer,zlim=c(-3,3)) > and >>imageplot(MA$M[,1],layout=list(ngrid.r=12,ngrid.c=4,nspot.r=21,nspot .c=21)) > > they all gave me the same kind of error messages: > Error in imageplot(log2(RB$Rb[, 1]), RB$printer, low = "white", high = > "red") : > Number of image spots does not agree with layout dimensions > > Or > Error in imageplot(MA$M[, 1], RB$printer) : > Number of image spots does not agree with layout dimensions > > Any idea is greatly appreciated! > Thanks > > ******************************** > Joyce Gu M.S. > Scientific Programmer > > Cancer Genomics Group > Baylor College of Medicine > Phone: 832-824-4680 > Fax: 832-825-4038