Question: Memory issues with limma and ImaGen file import
gravatar for CV Markus
12.5 years ago by
CV Markus10
CV Markus10 wrote:
Hallo Christian, ich hab genau dasselbe Problem, bei mir kommt die Meldung: "Fehler: kann Vektor der Gr??e 7179 Kb nicht allozieren" Am mem.limit() kann es nicht liegen, denn dann w?rde eine Meldung kommen, die darauf hinweist, dass das Speichermaximum erreicht ist. An der Art, wie die Daten eingelesen werden, kann es auch nicht liegen, ich verwende z.B. keine Textdateien, sondern eine Datenbankabfrage per ODBC und habe trotzdem das Problem. Hat sich das Problem bei Dir inzwischen gel?st? Gr??e, Markus Preisetanz Christian Spieth Wrote: ----------------------------- [BioC] Memory issues with limma and ImaGen file import Christian Spieth Christian.Spieth at Fri Apr 28 16:21:43 CEST 2006 * Previous message: [BioC] error running the example of the widget function in the widgetTools library * Next message: [BioC] Thoughts on computer purchase * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] 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\replicate 1\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 PGP fingerprint = 8A AC FD DA 57 A3 15 67 23 16 15 0A BD 04 AC A7 MD5 Fingerprint = 22a9627dcc5302371de7764b40c2be6d * Previous message: [BioC] error running the example of the widget function in the widgetTools library * Next message: [BioC] Thoughts on computer purchase * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about the Bioconductor mailing list
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