Hi Pierre,
I figured out what's wrong. I did not set the object unitNames.
After I ran
> unitNames <- getUnitNames(unf)
> units <- indexOf(unf,names=unitNames)
it works now.
Thanks,
Ying
On Wed, May 16, 2012 at 3:44 PM, Pierre Neuvial <pie...@stat.berkeley.edu>wrote:
> Hi,
>
> On Wed, May 16, 2012 at 9:05 PM, sean nj <njs...@gmail.com> 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 <njs...@gmail.com> 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 aroma-affymetrix@googlegroups.com
> >> 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 aroma-affymetrix@googlegroups.com
> > 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 aroma-affymetrix@googlegroups.com
> 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 aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
