Dear Christian, I have now identified the bug. It is fixed in limma 2.7.1 which should be available from CRAN in a couple of days. Thanks to Peter Morrison of biodiscovery.com who enabled me to find the bug by sending me some example data files. Best wishes Gordon >Date: Fri, 28 Apr 2006 16:21:43 +0200 >From: "Christian Spieth" <christian.spieth at="" uni-tuebingen.de=""> >Subject: [BioC] Memory issues with limma and ImaGen file import >To: <bioconductor at="" stat.math.ethz.ch=""> > >Hi, > >I am having a problem with limma 2.4.13 and ImaGene files: >Whenever I try to read the files as described in the manual > >targets <- readTargets() >files <- targets[,c("FileNameCy3","FileNameCy5")] >RG <- read.maimages(files, source ="imagene") > >R aborts the operation with the following error message: > > > RG <- read.maimages(files,source="imagene") >Read header information >Fehler: kann Vektor der Gr??e 3200000 Kb nicht allozieren >(Error: unable to allocate a vector of size 3200000 Kb) > >I am trying to read 10 chip files ( 5 replication with red and green). >Each file is approx. 6MB. Is there a special format of the ImaGene files? >My files start with > > >Begin Header > version 5.6.1 > Date Mon Apr 24 20:13:17 CEST 2006 > Image File >X:\Lab_Hochholdinger\Individual_folders\Diana\microarray\lrt\replicat e1\01Mu >rot\0G701Murot.tif > Page 0 > Page Name > Inverted false > Begin Field Dimensions > Field Metarows Metacols Rows Cols > A 8 4 20 20 > B 4 4 20 20 > End Field Dimensions > Begin Measurement parameters > Segmentation Method auto > Signal Low 0.0 > Signal High 0.0 > Background Low 0.0 > Background High 0.0 > Background Buffer 3.0 > Background Width 5.0 > End Measurement parameters > Begin Alerts > Control Type Minimum threshold If tested >Percentage allowed If failed Maximum threshold If tested >Percentage allowed If failed CV threshold If tested If >failed > End Alerts > Begin Quality settings > Empty Spots true Threshold: 2.0 > Poor Spots true > Begin Poor Spots Parameters > Background contamination flag true Threshold: >0.9995 > Background tested against subgrid data only true > Signal contamination flag false Threshold: >0.9995 > Signal contamination test connected to background >contamination threshold false > Ignored percentage flag true Threshold: 25.0 > Open perimeter flag true Threshold: 30.0 > Shape regularity flag true Threshold: 0.6 > Area To Perimeter Ratio flag false Threshold: >0.7 > Offset flag true Threshold: 60.0 > End Poor Spots Parameters > Negative Spots true > > End Quality settings >End Header >Begin Raw Data > Field Meta Row Meta Column Row Column Gene ID Flag >Signal Mean Background Mean Signal Median Background Median >Signal Mode Background Mode Signal Area Background Area Signal Total >Background Total Signal Stdev Background Stdev Shape >Regularity Ignored Area Spot Area Ignored Median Area To >Perimeter Open Perimeter XCoord YCoord Diameter Position >offset Offset X Offset Y Expected X Expected Y CM-X >CM-Y CM Offset CM Offset-X CM Offset-Y Min Diam Max >Diam Control Failed Control Background contamination present >Signal contamination present Ignored % failed Open perimeter >failed Shape regularity failed Perim-to-area failed Offset failed >Empty spot Negative spot Selected spot > A 1 1 1 1 HakeT2_V2-I-13-CB250166 0 >6628.6592 637.9275 6496.0 542.0 6694.4912 441.2314 >179.0 262.0 1186530.0 167137.0 2784.5909 466.856 >0.895 0.0 179.0 null 0.9763 0.0 1898.0 5548.0 16.0 >1.824 -0.7266 -1.673 1898.7266 5549.673 1898.3799 >5547.8547 1.851 -0.3467 -1.8183 14.7603 15.6522 0 0 >0 0 0 0 0 0 0 0 0 > >...... > > > > >The error happens both under Windows (1GB RAM) and Linux (4GB RAM). >Anyone an idea? > >Thanks in advance! > >christian > > >-- > Christian Spieth > Dipl.-Ing., MSc (Oxon) > Center for Bioinformatics (ZBIT), Univ. Tuebingen > NGFN - Nationales GenomForschungsNetz > Sand 1, D-72076 Tuebingen, Germany > Phone (+49/0) 7071 29 78987, Fax (+49/0) 7071 29 5091 >mailto:christian.spieth at uni-tuebingen.de > http://www-ra.informatik.uni-tuebingen.de > > PGP fingerprint = 8A AC FD DA 57 A3 15 67 23 16 15 0A BD 04 AC A7 MD5 > Fingerprint = 22a9627dcc5302371de7764b40c2be6d