Hi all I guess this question is mainly for matt richie but if anyone can tell me what I'm doing wrong... been using kooperberg correction for quite a while and had alot of success with it however with some new data I recieve the following error: > RG <- kooperberg(FILES, fg="median", bg="median", layout=LAYOUT) Error in .varaux2(x, i, j, ncols, nrows) : subscript out of bounds In addition: Warning message: data length [118] is not a sub-multiple or multiple of the number of rows [8] in matrix doesn't look like a problem with limma/kooperberg so its more likely to be my files however they read perfectly fine with read.maimages had a look at the gpr files and nothing is obviously wrong any ideas would be greatfully recieved using R (1.9.0) limma(1.6.7) -- -------------------------------- Jason Skelton Pathogen Microarrays Wellcome Trust Sanger Institute Hinxton Cambridge CB10 1SA Tel +44(0)1223 834244 Ext 7123 Fax +44(0)1223 494919

Hi Jason, Are the grids in your .gpr file all of the same size as specified in the layout argument? The kooperberg function assumes this and will produce an error like the one you are getting if they aren't. You might also have a problem doing print-tip loess normalization on this data if the layout argument and number of spots on the array don't agree. If this isn't the problem, perhaps you can send me one of your .gpr files and I'll take a more careful look. Best wishes, Matt Jason Skelton wrote: > Hi all > I guess this question is mainly for matt richie but if anyone can tell > me what I'm doing wrong... > been using kooperberg correction for quite a while and had alot of > success with it > however with some new data I recieve the following error: > > > RG <- kooperberg(FILES, fg="median", bg="median", layout=LAYOUT) > Error in .varaux2(x, i, j, ncols, nrows) : > subscript out of bounds > In addition: Warning message: > data length [118] is not a sub-multiple or multiple of the number of > rows [8] in matrix > > doesn't look like a problem with limma/kooperberg so its more likely > to be my files however > they read perfectly fine with read.maimages > had a look at the gpr files and nothing is obviously wrong > any ideas would be greatfully recieved > > using R (1.9.0) > limma(1.6.7)