Dear All, I have a problem of reading cel files from MOE430A type. The error I get is > library(affy) > res=justRMA() Error in just.rma(filenames = l$filenames, phenoData = l$phenoData, description = l$description, : Is c:/temp/mouse430a/Green.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats The first few lines of the cel file look like [CEL] Version=3 [HEADER] Cols=712 Rows=712 TotalX=712 TotalY=712 OffsetX=0 OffsetY=0 GridCornerUL=228 231 GridCornerUR=4490 217 GridCornerLR=4497 4487 GridCornerLL=235 4501 Axis-invertX=0 AxisInvertY=0 swapXY=0 DatHeader=[0..46130] Control 1 rerun:CLS=4733 RWS=4733 XIN=3 YIN=3 VE=17 2.0 02/07/04 11:41:58 MOE430A.1sq 6 Algorithm=Percentile AlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;Outli erLow:1.004 [INTENSITY] NumberCells=506944 My sessionInfo is R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] affy_1.22.0 Biobase_2.4.1 svGUI_0.9-43 svSocket_0.9-42 [5] svMisc_0.9-45 loaded via a namespace (and not attached): [1] affyio_1.12.0 preprocessCore_1.6.0 I appreicate any help. Thanks, Ming-chung Li [[alternative HTML version deleted]]

That does not seem to be a desirable situation. Given you have what looks to be a text format CEL file and that the parsers in affyio have been used with 1000s of text format CEL files (of many different chip types), it seems somewhat unlikely that it is an error in the parsing code, rather than some malformation of the CEL file. But, if you would like to send me this CEL file (off-list of course) I could examine it further. best, Ben On Mon, 2009-06-29 at 10:47 -0400, Ming-Chung Li wrote: > Dear All, > > I have a problem of reading cel files from MOE430A type. The error I get is > > > library(affy) > > res=justRMA() > > Error in just.rma(filenames = l$filenames, phenoData = l$phenoData, description = l$description, : > > Is c:/temp/mouse430a/Green.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats > > > > > The first few lines of the cel file look like > > [CEL] > > Version=3 > > [HEADER] > > Cols=712 > > Rows=712 > > TotalX=712 > > TotalY=712 > > OffsetX=0 > > OffsetY=0 > > GridCornerUL=228 231 > > GridCornerUR=4490 217 > > GridCornerLR=4497 4487 > > GridCornerLL=235 4501 > > Axis-invertX=0 > > AxisInvertY=0 > > swapXY=0 > > DatHeader=[0..46130] Control 1 rerun:CLS=4733 RWS=4733 XIN=3 YIN=3 VE=17 2.0 02/07/04 11:41:58 MOE430A.1sq 6 > > Algorithm=Percentile > > AlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;Out lierLow:1.004 > > [INTENSITY] > > NumberCells=506944 > > > My sessionInfo is > > R version 2.9.0 (2009-04-17) > > i386-pc-mingw32 > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > > [1] tcltk stats graphics grDevices utils datasets methods > > [8] base > > other attached packages: > > [1] affy_1.22.0 Biobase_2.4.1 svGUI_0.9-43 svSocket_0.9-42 > > [5] svMisc_0.9-45 > > loaded via a namespace (and not attached): > > [1] affyio_1.12.0 preprocessCore_1.6.0 > > > I appreicate any help. Thanks, > > Ming-chung Li > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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