Hi,
On Wed, May 16, 2012 at 9:05 PM, sean nj <[email protected]> wrote:
>
> 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'
> >
>
>From the error message (pretty explicit) it looks like you should have done
units <- indexOf(unf, names=unitNames)
instead of
units <- indexOf(unf, unitNames)
That's what you do below.
Cheers,
Pierre
> 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, 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]
> 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]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
