Hi, These scripts work OK for me on OSX (only on TXT CEL files, not the latest binary ones). I haven't gotten around to writing a version that uses the Fusion SDK. Mark celDate.sh #!/bin/bash # # Determine the date that the CEL file was created, from the CEL file header # eg "06/05/08 12:05:36" # # Mark Cowley, 2008-07-28 # grep -m1 -a '^DatHeader' "$@" | egrep -o '[0-9]{2}/[0-9]{2}/[0-9]{2} [0-9]{2}:[0-9]{2}:[0-9]{2}' -- or -- celDate.R # Extract the CEL file creation date stamp from within the CEL file header. # # Mark Cowley, 2008-07-29 celDate <- function(files) { stopifnot( all(file.exists(files)) ) files <- paste(squote(files), collapse=" ") cmd <- paste("grep -m1 -a '^DatHeader'", files, "| egrep -o '[0-9]{2}/[0-9]{2}/[0-9]{2} [0-9]{2}:[0-9]{2}:[0-9] {2}'") dates <- system(cmd, intern=T) dates } ----------------------------------------------------- Mark Cowley, PhD Peter Wills Bioinformatics Centre Garvan Institute of Medical Research, Sydney, Australia ----------------------------------------------------- On 22/09/2009, at 8:42 AM, Rob Dunne wrote: > Thanks for that. > > I am not using the development version yet but I will look out for > the new slot. > > Saroj, your method doesn't work for me, perhaps your cel file is > ascii? > strings SB_20D.CEL | grep DatHeader > > However, I have found > $ grep --text d.a.t.e. SB_20D.CEL > text/plainaffymetrix-scan-date(2008-04-03T04:45:53Z > > the "--text" option makes grep read a binary file as thought it was > text. I am not sure why I need the dots in date. > > Bye > Rob > > > > Patrick Aboyoun wrote: >> Robert, >> The answer depends on which version of R and BioC are you using. If >> you are using R <= 2.9, BioC <= 2.4, you will need to devise your >> own method; one of which was given by Saroj. If you are using R- >> devel and BioC 2.5 (devel), the eSet abstract class and its derived >> classes such as ExpressionSet contain a new slot called >> protocolData that contains an AnnotatedDataFrame object. This slot >> is to be populated by metadata contained in microarray data files. >> In BioC 2.5 (devel) the read.affybatch from affy and read.celfile >> from affyio add a ScanData column to the protocolData slot with the >> metadata you are looking for. >> Cheers, >> Patrick >> Saroj K Mohapatra wrote: >>> Hi Rob: >>> >>> I have a file called _16.CEL. I want to find out the date >>> information in its header. The following gives me: >>> >>> $ strings _16.CEL | grep DatHeader >>> DatHeader=[2..65534] _16:CLS=7365 RWS=7365 XIN=1 YIN=1 >>> VE=30 2.0 10/27/06 10:57:45 50207590 M10 I find a date >>> 10/27/06. Is this what you are looking for? >>> >>> Best, >>> >>> Saroj >>> >>> >>> Robert Dunne wrote: >>>> Hi List, >>>> >>>> I apologise for what may be a very simple question. How can I >>>> retrieve >>>> the scan date information from cel files? >>>> >>>> I can find the information using some editors, kate under linux >>>> shows >>>> "a f f y m e t r i x - s c a n - d a t e ( 2 0 0 8 - 0 4 - 0 3" >>>> but I can't find it all all using vi or emacs. I suppose this is >>>> something to do with encoding. >>>> Also "string file.cel | grep "d a t e"" does not work. >>>> >>>> I have tried the affxparser library but >>>> readCelHeader("file.cel") >>>> does not pick up the date. >>>> >>>> Unfortunately in many experiments the scan date turns out to be >>>> the major effect. >>>> >>>> Bye >>>> Rob >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> ------------------------------------------------------------------ ------ >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor