What does the following output:
library("R.filesets");
path <- Arguments$getReadablePath("rawData/C11/GenomeWideSNP_6/");
ds <- GenericDataFileSet$byPath(path);
print(ds);
print(lapply(ds, getFileSize));
/Henrik
On Fri, Feb 10, 2012 at 9:40 AM, Angelina Chattopadhyay Mukherjee
<angelina...@cancer.org.uk> wrote:
> Hi,
>
> Apologies for the delay in responding to your message. I'm afraid I am still
> struggling with the error. My subdirectory 'GenomeWideSNP_6' does contain
> .CEL files and I get the same error message. I'm sorry to trouble you again
> but could you please advise what I should do?
>
> Kind regards,
> Angelina
>
>
> ________________________________________
> From: aroma-affymetrix@googlegroups.com [aroma-affymetrix@googlegroups.com]
> On Behalf Of Henrik Bengtsson [henrik.bengts...@aroma-project.org]
> Sent: 02 February 2012 05:05
> To: aroma-affymetrix@googlegroups.com
> Subject: Re: [aroma.affymetrix] doCRMAv2 error
>
> Hi,
>
> first, I apologies that you had problems post your message; I just
> noticed that there were several messages "on hold" to be approved by
> the moderators. Normally we get a notice about this, but for some
> reason we didn't get it. Now to your question...
>
> On Fri, Jan 27, 2012 at 12:17 AM, Angelina Chattopadhyay Mukherjee
> <angelina...@cancer.org.uk> wrote:
>> Hi,
>>
>> I checked my annotation files and found I'm using the ones shown on the
>> aroma website: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl ,
>> GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp,
>> GenomeWideSNP_6,HB20080710.acs, GenomeWideSNP_6,Full.cdf.
>>
>> I'm using the correct directory structure as well.
>
> Even if I don't see it, I assume that the annotationData/ structure is
> correct, because otherwise you wouldn't have been able to setup the
> 'cdf' AffymetrixCdfFile object below.
>
>> I'd be grateful if anyone could help me with this error message:
>>
>>
>>> dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose);
>> 20120119 17:40:06|CRMAv2...
>> 20120119 17:40:06| CRMAv2/Setting up CEL set...
>> Error in list(`doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE, verbose
>> = verbose)` = <environment>, :
>>
>> [2012-01-19 17:40:06] Exception: Cannot create AffymetrixCelSet. No such
>> directory: C11/GenomeWideSNP_6
>
> This basically says that it cannot find directory
>
> rawData/C11/GenomeWideSNP_6/
>
> which should contain *.CEL files. Note that regardless of the CDF,
> the subdirectory should be "GenomeWideSNP_6/" (not
> "GenomeWideSNP_6,Full/").
>
> Hope this helps
>
> /Henrik
>
>> at throw(Exception(...))
>> at throw.default("Cannot create ", class(static)[1], ". No such directory:
>> ",
>> at throw("Cannot create ", class(static)[1], ". No such directory: ", path)
>> at method(static, ...)
>> at AffymetrixCelSet$byName(dataSet, ..., verbose = less(verbose, 50),
>> .onUnkno
>> at doCRMAv2.character(dataSet, cdf = cdf, combineAlleles = FALSE, verbose =
>> ve
>> at doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE, verbose = verbose)
>>
>>
>>
>> My session info is:
>>
>>> sessionInfo()
>> R version 2.14.1 (2011-12-22)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
>> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
>> [7] LC_PAPER=C LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] sfit_0.2.0 aroma.affymetrix_2.4.1 affxparser_1.26.2
>> [4] aroma.apd_0.2.0 R.huge_0.3.0 aroma.core_2.4.3
>> [7] aroma.light_1.22.0 matrixStats_0.4.3 R.rsp_0.7.1
>> [10] R.cache_0.5.2 R.filesets_1.1.4 digest_0.5.1
>> [13] R.utils_1.9.11 R.oo_1.8.3 R.methodsS3_1.2.1
>>
>>
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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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> You received this message because you are subscribed to the Google Groups
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> NOTICE AND DISCLAIMER
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> person(s). If you are not the intended recipient, notify the sender
> immediately, delete this email from your system and do not disclose or use
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>
> We may monitor all incoming and outgoing emails in line with current
> legislation. We have taken steps to ensure that this email and attachments
> are free from any virus, but it remains your responsibility to ensure that
> viruses do not adversely affect you.
> Cancer Research UK
> Registered in England and Wales
> Company Registered Number: 4325234.
> Registered Charity Number: 1089464 and Scotland SC041666
> Registered Office Address: Angel Building, 407 St John Street, London EC1V
> 4AD.
>
> --
> 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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--
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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