that is quick! thanks a lot!
cheers
jason
On Feb 11, 4:29 pm, Henrik Bengtsson <h...@stat.berkeley.edu> wrote:
> Update,
>
> I've updated affxparser so these warnings are no longer generated.
> When affxparser v1.15.4 becomes available on BioC devel, you can
> install it and these warnings will also go away.
>
> /Henrik
>
> On Tue, Feb 10, 2009 at 8:08 PM, Henrik Bengtsson <h...@stat.berkeley.edu>
> wrote:
> > Hi,
>
> > first of all, these warnings are ok and have no effect. There is no
> > need to convert your CEL files. The warnings only occur with CEL
> > files of the most recent Affymetrix Command Console (aka Calvin) file
> > format. If you do:
>
> > cf <- getFile(cstest, 1);
> > print(cf);
>
> > you will see that the CEL files are of this format.
>
> > DETAILS:
> > The warnings are generated when the timestamp of such CEL files are
> > read from the file header, i.e. when getTimestamp(cf) [on an
> > AffymetrixCelFile object] is called which in turn calls
> > readCcgHeader() in affxparser. The warnings are generated in the
> > latter in a few internal rawToChar() calls. I think it was from R
> > v2.8.0 that rawToChar() complains about converting raw vectors with
> > '\0' (you didn't get this warning before). I've updated
> > getTimestamp() to suppress these warnings (next release).
>
> > Cheers
>
> > /Henrik
>
> > On Tue, Feb 10, 2009 at 5:37 PM, Jason Li <jtj...@gmail.com> wrote:
>
> >> Why do i get all these warnings when "printing" binary CEL files?
> >> (Human promoter array)
>
> >> After i converted the files into text format using Affymetrix Power
> >> Tools, then there is no more warnings. But i thought binary files are
> >> supported?
>
> >> Thanks
> >> Jason Li
>
> >>> library(aroma.affymetrix)
> >>> verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> >>> chipType <- "Hs_PromPR_v02"
> >>> cdf <- AffymetrixCdfFile$byChipType(chipType, verbose=-80)
> >>> cstest <- AffymetrixCelSet$byName("TESTBINARY", cdf=cdf, verbose=verbose)
>
> >>> print(cstest)
> >> AffymetrixCelSet:
> >> Name: TESTBINARY
> >> Tags:
> >> Path: rawData/TESTBINARY/Hs_PromPR_v02
> >> Platform: Affymetrix
> >> Chip type: Hs_PromPR_v02
> >> Number of arrays: 4
> >> Names: MD7485_2420_T1_(Hs_PromPR_v02), MD7485_2420_T2_(Hs_PromPR_v02),
> >> MD7486_2411_T1_(Hs_PromPR_v02), MD7486_2411_T2_(Hs_PromPR_v02)
> >> Time period: 2008-07-10 11:52:15 -- 2008-07-10 16:14:35
> >> Total file size: 179.38MB
> >> RAM: 0.01MB
> >> There were 36 warnings (use warnings() to see them)
> >>> warnings()
> >> Warning messages:
> >> 1: In rawToChar(raw) ... :
> >> truncating string with embedded nul:
> >> 'Hs_PromPR_v02\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 2: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Universal
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 3: In rawToChar(raw) ... :
> >> truncating string with embedded nul:
> >> 'Hs_PromPR_v02\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 4: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Hs_PromPR_v02_MASTER
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 5: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Auto aligned
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 6: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Universal
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 7: In rawToChar(raw) ... :
> >> truncating string with embedded nul: ' MD7485_2420 T1_
> >> (Hs_PromPR_v02):CLS=16488RWS=16488XIN=0 YIN=0 VE=0 0
> >> 07/10/08 15:07:00 50205260 M10 \024 \024 Hs_PromPR_v02.1sq \024
> >> \024 \024 \024 \024 570 \024 25064.757813 \024 3.500000 \024 0.7000
> >> \024
> >> 3\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 8: In rawToChar(raw) ... :
> >> truncating string with embedded nul: '6340d375-3339-484f-
> >> bd02-0a761c00dd67\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 9: In rawToChar(raw) ... :
> >> truncating string with embedded nul:
> >> '@51140500646985121708403729068595\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 10: In rawToChar(raw) ... :
> >> truncating string with embedded nul:
> >> 'Hs_PromPR_v02\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 11: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Universal
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 12: In rawToChar(raw) ... :
> >> truncating string with embedded nul:
> >> 'Hs_PromPR_v02\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 13: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Hs_PromPR_v02_MASTER
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 14: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Auto aligned
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 15: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Universal
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 16: In rawToChar(raw) ... :
> >> truncating string with embedded nul: ' MD7485_2420 T2_
> >> (Hs_PromPR_v02):CLS=16398RWS=16398XIN=0 YIN=0 VE=0 0
> >> 07/10/08 14:44:25 50205260 M10 \024 \024 Hs_PromPR_v02.1sq \024
> >> \024 \024 \024 \024 570 \024 25072.263672 \024 3.500000 \024 0.7000
> >> \024
> >> 3\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 17: In rawToChar(raw) ... :
> >> truncating string with embedded nul: '55844f0f-1b6c-47c2-99de-
> >> d7d149be0d8c\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 18: In rawToChar(raw) ... :
> >> truncating string with embedded nul:
> >> '@51140500646985121708403729068582\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 19: In rawToChar(raw) ... :
> >> truncating string with embedded nul:
> >> 'Hs_PromPR_v02\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 20: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Universal
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 21: In rawToChar(raw) ... :
> >> truncating string with embedded nul:
> >> 'Hs_PromPR_v02\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 22: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Hs_PromPR_v02_MASTER
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 23: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Auto aligned
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 24: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Universal
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 25: In rawToChar(raw) ... :
> >> truncating string with embedded nul: ' MD7486_2411 T1_
> >> (Hs_PromPR_v02):CLS=16445RWS=16445XIN=0 YIN=0 VE=0 0
> >> 07/10/08 16:14:35 50205260 M10 \024 \024 Hs_PromPR_v02.1sq \024
> >> \024 \024 \024 \024 570 \024 25062.904297 \024 3.500000 \024 0.7000
> >> \024
> >> 3\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 26: In rawToChar(raw) ... :
> >> truncating string with embedded nul: '6acd5a66-37cc-4f6d-
> >> b1f5-1702216b4588\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 27: In rawToChar(raw) ... :
> >> truncating string with embedded nul:
> >> '@51140500646985121708403729068605\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 28: In rawToChar(raw) ... :
> >> truncating string with embedded nul:
> >> 'Hs_PromPR_v02\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 29: In rawToChar(raw) ... :
> >> truncating string with embedded nul: 'Universal
> >> \0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> >> 30: In rawToChar(raw) ... :
> >> truncating string with embedded nul:
>
> ...
>
> read more »
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