This is where i ran the above code:
aroma.affymetrix v1.0.0 (2009-01-12)
R version 2.8.0 (2008-10-20)
the CDFs are downloaded from
http://groups.google.com/group/aroma-affymetrix/web/hs-prompr-v02-human-promoter-tiling-1-0r
On Feb 11, 12:37 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:
> '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'
> 31: 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'
> 32: 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'
> 33: 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'
> 34: In rawToChar(raw) ... :
> truncating string with embedded nul: ' MD7486_2411 T2_
> (Hs_PromPR_v02):CLS=16401RWS=16401XIN=0 YIN=0 VE=0 0
> 07/10/08 11:52:15 50205260 M10 \024 \024 Hs_PromPR_v02.1sq \024
> \024 \024 \024 \024 570 \024 25057.587891 \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'
> 35: In rawToChar(raw) ... :
> truncating string with embedded nul: 'e3f8132e-b1d1-425f-bb59-
> d32fee7569f4\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
> 36: In rawToChar(raw) ... :
> truncating string with embedded nul:
> '@51140500646985121708403729068602\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0'
>
>
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