Hi guys,
I was following the Vignette: Creating binary data files containing copy
number estimates and trying to work on agilent HG-CGH-244A chip. I
downloaded and unzipped the .gz of the
HG-CGH-244A,TCGA,HB20080512,unitNames.txt and
HG-CGH-244A,TCGA,HB20080512.ugp and put them in
H:\Aroma_Analysis\annotationData\chipTypes\HG-CGH-244A folder. Then I tried
to run the same code on the vignette and got the error right away (please
see end of this email). Did I do something wrong?
I have one more question regarding "Creating data files containing log2 CN
ratios" with HG-CGH-244A chip. The data I have are level 2 files from TCGA.
There is one txt file for each sample (not the original .asb file) and its
format is like:
Hybridization REF MSK_00001_251469322729_S01_CGH-v4_91
Composite Element REF normalizedLog2Ratio
A_14_P112718 0.135431541355747
A_16_P15000916 0.441719513563848
A_16_P15001074 0.227252175271962
A_16_P00000012 0.231158251618718
A_16_P00000014 -0.0623833233443793
.........................................................
..........................................................
My first question is, does this kind data file work?
My second question is, do I need to create a folder rawCnData as mentioned
in the vignette (Pathname:
rawCnData/MyDataSet,tagA,tagB/HG-CGH-244A/SampleA,tagA,tagB,log2ratio,total.asb)?
I also have the rawData folder which holds affy snp6 and expression data.
Thanks a lot for the help!
Ying
> library(aroma.core)
> chipType <- "HG-CGH-244A"
> unf <- TextUnitNamesFile$byChipType(chipType)
Error in method(static, ...) :
[2012-05-15 12:12:26] Exception: Failed to create TextUnitNamesFile object.
Could to locate an annotation data file for chip type 'HG-CGH-244A'
(without requiring any tags) and with filename extension 'names' (this may
not be the correct extension as it was guessed from the class name
'TextUnitNamesFile').
at #02. method(static, ...)
- method() is in environment 'aroma.core'
at #01. TextUnitNamesFile$byChipType(chipType)
- TextUnitNamesFile$byChipType() is local of the calling function
> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252 LC_MONETARY=English_United States.1252
LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.core_2.5.0 aroma.light_1.24.0 matrixStats_0.5.0
R.rsp_0.7.5 R.filesets_1.1.5 digest_0.5.2 R.cache_0.6.2
R.utils_1.12.1
[9] R.oo_1.9.3 R.methodsS3_1.2.2
>
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