Hello Henrik,
On Tue, Jun 7, 2011 at 10:11 AM, Henrik Bengtsson <
henrik.bengts...@aroma-project.org> wrote:
> Hi,
>
> first of all, indexOf(cdf, pattern="") does indeed work, e.g.
>
> > cdf <- AffymetrixCdfFile$byChipType("Mapping10K_Xba142");
> > units <- indexOf(cdf, pattern="");
> > str(units)
> int [1:10208] 1 2 3 4 5 6 7 8 9 10 ...
>
> Your 'cdfT' object seems not to be what you think it is, i.e. it is
> not an AffymetrixCdfFile object. It seems to be a simple string
> ("character").
>
Yes it was,
>
> I don't think your problem is related to updates in aroma.affymetrix.
> However, the underlying error may be caught earlier now, so you end up
> getting a different error.
>
Yes now its working
>
> Also, I don't know what the "SPACE script / ComputeGmatrix" comes from
> - is that something you wrote or someone else? If someone else, wrote
> it, have you checked with that person?
>
It was a problem of CDFs and now the scripts are working as i build CDF
again. That scripts are from SPACE package(Anton et al. BMC Bioinformatics
2010, 11:578).
Thanks a lot,
Ravi
> Cheers,
>
> Henrik
>
>
> On Mon, May 30, 2011 at 2:24 AM, Ravi Sharma <rdsharm...@gmail.com> wrote:
> >
> > 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.
> >> >
> >> >
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> >> >
> >>
> >> --
> >> 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.
> >>
> >>
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> >
> >
> >
> > --
> >
> > --
> > 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/
