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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