Dear All, I'm interested in identifying CNV regions using two Nimblegen arrays - both of which are input vs input arrays. A suitable package, I think, is snapCGH. I'm pretty new to both R and array analysis, however, I came across a post in the BioC mailing list, which included two R scripts (processNimblegenData.R and NimblegenUtilityFunctions.R), that utilised snapCGH and which seemed to do what I was after. I worked my way through the commands in processNimblegenData.R. Unfortunately I got the following error when I tried to run the processCGH method: Error in `row.names<-.data.frame`(`*tmp*`, value = c(1L, 0L)) : invalid 'row.names' length I had previously received warnings after a couple of other commands: NimblegenHeatmaps(RG) Processing heat maps... G:ChipNo = 1 (ChipID = 8898202_532.pair ) Error in image.default(x = (-1:770), y = (-1:1026), z = zmat, col = col, : dimensions of z are not length(x)(-1) times length(y)(-1) RG <- readPositionalInfo(RG, source = "nimblegen") Warning message: In data.frame(input$genes, Chr = as.numeric(chr), Start = (as.numeric(start)/1e+06), : NAs introduced by coercion If it helps, my MAlist object looks like this: An object of class "MAList" $genes IMAGE_ID GENE_EXPR_OPTION SEQ_ID PROBE_ID 829 8898202_532 BLOCK1 chr11:60023467-60024667 CHR11FS060023489 830 8898202_532 BLOCK1 chr11:60023467-60024667 CHR11FS060023569 831 8898202_532 BLOCK1 chr11:60023467-60024667 CHR11FS060023674 832 8898202_532 BLOCK1 chr11:60023467-60024667 CHR11FS060023764 833 8898202_532 BLOCK1 chr11:60023467-60024667 CHR11FS060023839 Position X Y MATCH_INDEX SEQ_URL Chr Start End 829 60.02349 253 327 71842416 NA NA 60.02349 60.02349 830 60.02357 48 92 71842417 NA NA 60.02357 60.02357 831 60.02367 61 95 71842418 NA NA 60.02367 60.02367 832 60.02376 299 87 71842419 NA NA 60.02376 60.02376 833 60.02384 215 433 71842420 NA NA 60.02384 60.02384 71204 more rows ... $design [1] -1 -1 $M 8898202_532.pair 8898302_532.pair [1,] 0.4152331 0.19290427 [2,] 0.1847667 0.39225230 [3,] 0.1450361 0.01751499 [4,] 0.2403561 -0.06698188 [5,] 0.2845034 0.12658724 71204 more rows ... $A 8898202_532.pair 8898302_532.pair [1,] 10.58601 10.43860 [2,] 10.44993 10.32034 [3,] 10.41355 10.09611 [4,] 10.48482 10.13966 [5,] 10.63333 10.50491 71204 more rows ... I was wondering whether anyone had any idea as to how I could overcome these issues. Any help would be appreciated. Many Thanks Gareth. ----- Dr Gareth A Wilson Medical Genomics Group UCL Cancer Institute Paul O'Gorman Building University College London 72 Huntley Street London WC1E 6BT tel: +44 (0) 20 7679 0999 ----- ********************************************************************** This email and any files transmitted with it are confide...{{dropped:6}}