Hi,
I did get rid of the error message when I ran :
> unf <- TextUnitNamesFile$byChipType(chipType)
I got this done by loading the aroma.affymetrix package, in addition to
aroma.core.
But now I got another error message when I followed Henrik's code at
http://aroma-project.org/node/88
I was trying to creating data files containing log2 CN ratios. Everything
was fine until I ran
> units <- indexOf(unf, unitNames)
Error in indexOf.UnitNamesFile(unf, unitNames) :
[2012-05-16 14:53:18] Exception: If specified, argument 'pattern' must be a
single string. Did you mean to use argument 'names'?
at #02. indexOf.UnitNamesFile(unf, unitNames)
- indexOf.UnitNamesFile() is in environment 'aroma.core'
at #01. indexOf(unf, unitNames)
- indexOf() is in environment 'R.filesets'
>
The command ran successfully when I tried to get units for certain probes
> units <- indexOf(unf, names=c("A_16_P15025341","A_16_P00013121")
+ )
> units
[1] 1006 1019
>
I tried > ?indexOf.UnitNamesFile() and here is what I got:
indexOf(this, pattern=NULL, names=NULL, ...) Arguments
pattern A pattern to be used for identifying unit names of interest. If
NULL <http://127.0.0.1:16952/library/base/html/NULL.html>, no regular
expression matching is done.
names Names to be match exactly to the unit names.
... Not used.
What did I do wrong?
Thanks a lot for the help!
Ying
> 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
[3] 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.affymetrix_2.5.0 affxparser_1.28.0 aroma.apd_0.2.2
R.huge_0.3.0
[5] aroma.core_2.5.0 aroma.light_1.24.0 matrixStats_0.5.0
R.rsp_0.7.5
[9] R.filesets_1.1.5 digest_0.5.2 R.cache_0.6.2
R.utils_1.12.1
[13] R.oo_1.9.3 R.methodsS3_1.2.2
loaded via a namespace (and not attached):
[1] tools_2.15.0
>
On Tue, May 15, 2012 at 12:38 PM, sean nj <[email protected]> wrote:
> 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
> >
>
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [email protected]
> To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to [email protected]
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