Hi,
please let us know what your source of documentation is, e.g.
webpages, because you are using method names that are either outdated
or non-public. Then I'll answer your questions...
/Henrik
On Tue, Mar 9, 2010 at 10:44 PM, dkny169 <daniela...@yahoo.com> wrote:
> Hi Mark,
> Thanks for your answer. I think it works now; I had the working
> directory set at chipTypes and not at the parent directory of
> annotationData.
> I am getting following back:
>> cdf<-AffymetrixCdfFile$findByChipType("MoEx-1_0-st-v1")
>> cdf
> [1] "annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1.cdf"
>
> I am trying to upload the CEL files now that are stored in rawData/
> tissues/MoEx-1_0-st-v1. The working directory is set at the parent
> directory of rawData. But again I am getting a failure message. What
> am I doing wrong now?
> cs<-AffymetrixCelSet$fromName("tissues",cdf=cdf)
> Error in list(`AffymetrixCelSet$fromName("tissues", cdf = cdf)` =
> <environment>, :
>
> [2010-03-09 16:28:12] Exception: AffymetrixCelSet$fromName() is
> defunct. Use AffymetrixCelSet$byName() instead.
> at throw(Exception(...))
> at throw.default(msg)
> at throw(msg)
> at method(static, ...)
> at AffymetrixCelSet$fromName("tissues", cdf = cdf)
>> cs<-AffymetrixCelSet$byName("tissues",cdf=cdf)
> Error in list(`AffymetrixCelSet$byName("tissues", cdf = cdf)` =
> <environment>, :
>
> [2010-03-09 16:38:21] Exception: Argument 'cdf' is neither of nor
> inherits class AffymetrixCdfFile: character
> at throw(Exception(...))
> at throw.default(sprintf("Argument '%s' is neither of nor inherits
> class %s: %
> at throw(sprintf("Argument '%s' is neither of nor inherits class %s:
> %s", .nam
> at method(static, ...)
> at Arguments$getInstanceOf(cdf, "AffymetrixCdfFile")
> at method(static, ...)
> at AffymetrixCelSet$byName("tissues", cdf = cdf)
>
> Thanks,
> Daniela
>
>
> On Mar 9, 3:23 pm, "Mark Robinson" <mrobin...@wehi.edu.au> wrote:
>> Hi Daniela.
>>
>> Is your CDF in the:
>>
>> annotationData/chipTypes/MoEx-1_0-st-v1/
>>
>> directory?
>>
>> (http://aroma-project.org/node/66)
>>
>> Cheers,
>> Mark
>>
>>
>>
>> > Hi,
>> > I stored my CDF file in annotationData/chipTypes; nevertheless I cannot
>> > upload the file.
>> > Can anyone please tel me what I am doing wrong:
>>
>> > cdf<-AffymetrixCdfFile$byChipType("MoEx-1_0-st-v1.cdf")
>>
>> > ror in list(`AffymetrixCdfFile$byChipType("MoEx-1_0-st-v1.cdf")` =
>> > <environment>, :
>> >
>> > [2010-03-09 14:50:58] Exception: Could not locate a file for this chip
>> > type: MoEx-1_0-st-v1.cdf
>> > at throw(Exception(...))
>> > at throw.default("Could not locate a file for this chip type: ",
>> > paste(c(chipT
>> > at throw("Could not locate a file for this chip type: ",
>> > paste(c(chipType, tag
>> > at method(static, ...)
>> > at AffymetrixCdfFile$byChipType("MoEx-1_0-st-v1.cdf")
>>
>> > Many thanks for your help!
>>
>> > --
>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
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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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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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