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").
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.
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?
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.
>> >
>> >
>> > You received this message because you are subscribed to the Google
>> > Groups
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>> > 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
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>> 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/.
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To unsubscribe and other options, go to http://www.aroma-project.org/forum/
