Hi, We are trying to extract the header info in the affy CEL files, particularly the scan date and time and the scanner serial number. The affyxparser:readCelHeader and affyio:read.celfile.header function works fine for the text and binary CEL files. However when I tried them on the AGCC generated CEL files, the header slots are empty. Is there a way to obtain such info for the AGCC CEL files? Thank you very much! Yiwen He NIH/CIT/DCB/BIMAS

AFFXPARSER: There is readCcgHeader() that allows you to access the header of such CEL files too (please note that this function is a working beta that does not utilize Fusion SDK, but was coded up for internal test reasons). AROMA.AFFYMETRIX: Alternatively, you can use the high-level API of aroma.affymetrix (on CRAN) package to do this for you: library("aroma.affymetrix"); dsR <- AffymetrixCelSet$byName("HapMap270,6.0,CEU,testSet", chipType="GenomeWideSNP_6"); print(dsR); AffymetrixCelSet: Name: HapMap270 Tags: 6.0,CEU,testSet Path: rawData/HapMap270,6.0,CEU,testSet/GenomeWideSNP_6 Platform: Affymetrix Chip type: GenomeWideSNP_6 Number of arrays: 6 Names: NA06985, NA06991, ..., NA07019 Time period: 2007-03-06 12:13:04 -- 2007-03-06 19:17:16 Total file size: 395.13MB RAM: 0.01MB pathnames <- getPathnames(dsR); str(pathnames); Named chr [1:6] "C:/Users/hb/Documents/My Data/rawData/HapMap270,6.0,CEU,testSe t/GenomeWideSNP_6/NA06985.CEL" ... - attr(*, "names")= chr [1:6] "NA06985" "NA06991" "NA06993" "NA06994" ... ts <- getTimestamps(dsR); print(ts); [1] "2007-03-06 12:13:04 PST" "2007-03-06 16:15:53 PST" [3] "2007-03-06 19:17:16 PST" "2007-03-06 17:05:24 PST" [5] "2007-03-06 17:38:23 PST" "2007-03-06 15:12:49 PST" str(ts); POSIXlt[1:9], format: "2007-03-06 12:13:04" "2007-03-06 16:15:53" ... File by file: df <- getFile(dsR, 2); print(df); AffymetrixCelFile: Name: NA06991 Tags: Full name: NA06991 Pathname: rawData/HapMap270,6.0,CEU,testSet/GenomeWideSNP_6/NA06991.CEL File size: 65.85 MB (69045921 bytes) RAM: 0.01 MB File format: v1 (binary; CC) Platform: Affymetrix Chip type: GenomeWideSNP_6 Timestamp: 2007-03-06 16:15:53 ts <- getTimestamp(df); print(ts); [1] "2007-03-06 16:15:53" str(ts) POSIXlt[1:9], format: "2007-03-06 16:15:53" /Henrik On Wed, Jan 6, 2010 at 12:06 PM, He, Yiwen (NIH/CIT) [C] <heyiwen at="" mail.nih.gov=""> wrote: > Hi, > > We are trying to extract the header info in the affy CEL files, particularly the scan date and time and the scanner serial number. The affyxparser:readCelHeader and affyio:read.celfile.header function works fine for the text and binary CEL files. However when I tried them on the AGCC generated CEL files, the header slots are empty. Is there a way to obtain such info for the AGCC CEL files? > > Thank you very much! > > Yiwen He > NIH/CIT/DCB/BIMAS > > _______________________________________________ > 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 >