I am hoping someone can tell me what is causing this problem. I am using R 2.1.0, limma 2.0.2 on a Windows 2000 system. I have four .txt files containing 2-color microarray data. If I read each individual txt file it seems to work, but when I try to read all of the files I get the error shown below: > RG=read.maimages("C1_vs_O1.txt",columns=list(Rf="Spot Median Intensity (w685)",Gf="Spot Median Intensity (w595)",Rb="Background Median Intensity (w685)",Gb="Background Median Intensity (w595)")) Read C1_vs_O1.txt (seems OK) > RG=read.maimages(ext="txt",columns=list(Rf="Spot Median Intensity (w685)",Gf="Spot Median Intensity (w595)",Rb="Background Median Intensity (w685)",Gb="Background Median Intensity (w595)")) Read C1_vs_O1.txt Error in "[<-"(`*tmp*`, , i, value = c(168, 175, 265, 313, 32495, 32475, : number of items to replace is not a multiple of replacement length The first four lines in the file C1_vs_O1.txt are: Number Name Array/Plate Flagged As Control Spot Multi- Set Multi-Set Row Multi-Set Column Set Set Row Set Column Row Column Comments Clone ID UniGene cluster ID Gene symbol Locus ID Chromosome ID GenBank accession number Tissue Gene map Gene name Organism Sequence Detection Method (w595) Detection Method (w685) Detection Status (w595) Detection Status (w685) X Centroid (pixels) (w595) X Centroid (pixels) (w685) Y Centroid (pixels) (w595) Y Centroid (pixels) (w685) X Spot Deviation (um) (w595) X Spot Deviation (um) (w685) Y Spot Deviation (um) (w595) Y Spot Deviation (um) (w685) X Set Deviation (um) (w595) X Set Deviation (um) (w685) Y Set Deviation (um) (w595) Y Set Deviation (um) (w685) Major Extent (um) (w595) Major Extent (um) (w685) Minor Extent (um) (w595) Minor Extent (um) (w685) Compactness (%) (w595) Compactness (%) (w685) Threshold (w595) Threshold (w685) Spot Saturation (%) (w595) Spot Saturation (%) (w685) Spot Mean Intensity (w595) Spot Mean Intensity (w685) Spot Median Intensity (w595) Spot Median Intensity (w685) Spot Standard Deviation (w595) Spot Standard Deviation (w685) Spot Number of Pixels (w595) Spot Number of Pixels (w685) Spot Total Intensity (w595) Spot Total Intensity (w685) Spot Peak Intensity (w595) Spot Peak Intensity (w685) Background Mean Intensity (w595) Background Mean Intensity (w685) Background Median Intensity (w595) Background Median Intensity (w685) Background Standard Deviation (w595) Background Standard Deviation (w685) Background Number of Pixels (w595) Background Number of Pixels (w685) Spot Confidence (w595) Spot Confidence (w685) Spot Normalized Intensity (w595) Spot Normalized Intensity (w685) Spot Ratio (w595) Spot Ratio (w685) Spot SNR (w595) Spot SNR (w685) Spot CV (%) (w595) 1 A1_AB IGERT_C1vsO1_11_10_04 NORMAL NO 1 1 1 A 1 1 1 1 None None None None None None None None None None None None AUTO AUTO DETECTED DETECTED 122.388885 122.388885 19.125 19.125 13.961801 13.961801 -7.780155 -7.780155 -9.756 -9.756 0 0 10.134623 10.134623 9.486059 9.486059 34.932919 34.932919 338 338 0 0 225.117279 117.413582 216 115 40.293694 25.080153 162 162 36469 19021 317 184 174.990311 86.96489 174 86 15.307359 12.753221 826 826 100 100 42 29 1.448276 0.690476 3.274698 2.38753 74.356911 2 A1_AB IGERT_C1vsO1_11_10_04 NORMAL NO 1 1 1 A 1 1 1 2 None None None None None None None None None None None None AUTO AUTO DETECTED DETECTED 150.583328 150.583328 19.666666 19.666666 17.027 17.027 -2.151189 -2.151189 -9.756 -9.756 0 0 10.197981 10.197981 9.409546 9.409546 46.076748 46.076748 377 377 0 0 252.658386 129.621124 239 124 46.958637 25.637608 161 161 40678 20869 404 229 197.486191 101.923172 197 103 19.706385 15.429781 833 833 100 100 42 21 2 0.5 2.799712 1.795097 77.255592 3 A2_AB IGERT_C1vsO1_11_10_04 NORMAL NO 1 1 1 A 1 1 1 3 None None None None None None None None None None None None AUTO AUTO DETECTED DETECTED 177.301987 177.301987 18.797029 18.797029 5.694523 5.694523 -10.29089 -10.29089 -9.756 -9.756 0 0 11.567095 11.567095 9.996995 9.996995 19.474066 19.474066 521 521 0 0 400.362488 219.306244 393 213 108.947014 62.532211 160 160 64058 35089 685 387 228.681213 121.866669 224 119 29.274176 18.376568 825 825 100 100 169 94 1.797872 0.556213 5.864598 5.302382 61.125092 If anyone can tell me how to get around this problem I would be grateful for the help! Thanks, Susan J. Miller Biotechnology Computing Facility Arizona Research Laboratories University of Arizona Tucson, AZ 85721 (520) 626-2597