Hello, #
Here is the session Information:
>sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-redhat-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] SPACE_1.0 combinat_0.0-8 graph_1.28.0
[4] MASS_7.3-9 aroma.affymetrix_2.1.1 aroma.apd_0.1.8
[7] affxparser_1.22.1 R.huge_0.2.2 aroma.core_2.1.1
[10] aroma.light_1.18.4 matrixStats_0.2.2 R.rsp_0.5.4
[13] R.cache_0.4.2 R.filesets_1.0.2 digest_0.4.2
[16] R.utils_1.7.6 R.oo_1.8.0 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] tools_2.12.1
#
I was running the SPACE script (ComputeGmatrix) to generate G and GE
matrices with aroma.affymetrix_2.1.1. I got the following error:
>Glist<-ComputeGmatrix(cdfG,cdfT)
Reading indexes for genes...done
Reading indexes for units (units(G)=transcripts units(GE)=exons)...Error in
UseMethod("indexOf") :
no applicable method for 'indexOf' applied to an object of class "character"
#
Than, i run the source code of ComputeGmatrix (Source code is attached with
mail) and i got the following error.
>unitsT <- indexOf(cdfT, pattern='')
Error in UseMethod("indexOf") :
no applicable method for 'indexOf' applied to an object of class "character"
#
However, in case of cdfG it is working:
> unitsG <- indexOf(cdfG, pattern='')
#
'CDFs' information are given here:
> cdfG
AffymetrixCdfFile:
Path: annotationData/chipTypes/hjay
Filename: hjay,r1.cdf
Filesize: 107.39MB
Chip type: hjay,r1
RAM: 1.81MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 33845
Cells per unit: 193.64
Number of QC units: 0
> cdfT
AffymetrixCdfFile:
Path: annotationData/chipTypes/hjay
Filename: hjay,r1,tr,9.cdf
Filesize: 233.38MB
Chip type: hjay,r1,tr,9
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 83374
Cells per unit: 78.60
Number of QC units: 0
#
With previously version of aroma.affymetrix i was getting the wrong indices
in script ComputeGmatrix (a small part of script is below)
> patternT=''
>cat("Reading indexes for units (units(G)=transcripts units(GE)=exons)...");
>unitsT <- indexOf.UnitNamesFile(cdfT, pattern=patternT)
>transcripts <- getUnitNames(cdfT, units=unitsT)
>indicesT <- getCellIndices(cdfT,units=unitsT)
so i updated the version of aroma.affyemtrix, and now i am not able to get
even units name for cdfT.
regards,
Ravi
On Fri, May 27, 2011 at 8:20 PM, Henrik Bengtsson <
henrik.bengts...@aroma-project.org> wrote:
> Hi,
>
> please provide you full script showing what you are trying to do and
> where you get errors. Don't forget to also report your sessionInfo().
> Please all give the full details of the CDFs you are referring to.
>
> /Henrik
>
> On Fri, May 27, 2011 at 4:22 AM, Ravi Sharma <rdsharm...@gmail.com> wrote:
> >
> > Dear,
> >
> > Let me describe from beginning, I was facing the problem of wrong cell
> > indeces using 'getCellIndices' command (with an older version of
> > aroma.affymetrix) but i was able to retrieve the indeces. After some
> search,
> > i found that new version of aroma.affymetrix 2.1.0 perhaps 2.0.6 has
> > resolved this problem. So i have updated the aroma.affymetrix version.
> > Now i can' not even retrieve the index of Units using "indexof" commnand
> the
> > error message is :
> >
> > no applicable method for 'indexOf' applied to an object of class
> "character"
> >
> > Probably that correspond to the CDF file:
> > I am using 3 CDFs:
> > For 1) Gene 2) Transcript 3) exons
> >
> > I tried "indexof" command with gene CDF and its working because
> (probably)
> > Units are in numeric format, However, failed with concern of transcript
> and
> > Exon CDFs probably 'alpha numeric' format of Units.
> >
> > any possible suggestion?
> >
> >
> >
> > regards,
> > Ravi
> >
> >
> > --
> > 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/
ComputeGmatrix.R
Description: Binary data
