HI Henrik,
I could able to resolve my problem wrt CDF files but now i am struck with
following error.
> cs <- AffymetrixCelSet$byName("tissues", cdf=cdf)
Error in list(`AffymetrixCelSet$byName("tissues", cdf = cdf)` =
<environment>, :
[2010-08-05 13:38:14] Exception: Cannot create AffymetrixCelSet. No such
directory: tissues/HuGene-1_0-st-v1
at throw(Exception(...))
at throw.default("Cannot create ", class(static)[1], ". No such
directory: ", path)
at throw("Cannot create ", class(static)[1], ". No such directory: ",
path)
at method(static, ...)
at AffymetrixCelSet$byName("tissues", cdf = cdf)
>
I would like to know what directory i should create for getting rid of this
error
Thanks
Vish
On Thu, Aug 5, 2010 at 1:10 PM, ashwin Vishnuvardhana <
ashwin4bioinformat...@gmail.com> wrote:
> HI but still I have a problem, These are steps i am doing
>
> 1. My current directory is on desktop where exactly my raw data is
> 2. then I am trying to use the command in aroma.project
> 3. I did changed the directory as you mentioned
>
> And the error remains same. I have one question do we convert cdf (text)
> file to binary ? I downloaded it from aroma project website.
>
> Thanks
> Vish
>
>
> On Thu, Aug 5, 2010 at 12:38 PM, Henrik Bengtsson
> <h...@stat.berkeley.edu>wrote:
>
>> Hi,
>>
>> you write:
>>
>> annotationData/Chip type/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.CDF
>>
>> but that is *not* was is documented or written in the vignettes. You
>> should have:
>>
>> annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.CDF
>>
>> It is really important that you use the correct directory names
>> exactly like that.
>>
>> /Henrik
>>
>> On Thu, Aug 5, 2010 at 7:34 PM, ashwin Vishnuvardhana
>> <ashwin4bioinformat...@gmail.com> wrote:
>> > HI Pierre,
>> > I did saved in the similar way (aroma.affymetrix/annotationData/Chip
>> > type/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.CDF)
>> > but still i am coming up with same error.
>> >
>> > Thanks
>> > Vish
>> >
>> > On Tue, Aug 3, 2010 at 5:32 PM, Pierre Neuvial <
>> pie...@stat.berkeley.edu>
>> > wrote:
>> >>
>> >> Hi,
>> >>
>> >> Most probably you haven't put the required CDF file in the
>> >> corresponding annotationData/chipTypes/ directory.
>> >>
>> >> Have you read the vignette http://aroma-project.org/node/38 ? This is
>> >> well explained there.
>> >>
>> >> Also, similar versions of this question have been answered on this
>> >> list, see for example
>> >>
>> >>
>> http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/d992f2ca51e71774/8ba42bb7bdbf1b48
>> >>
>> >> Best
>> >>
>> >> Pierre.
>> >>
>> >>
>> >> Be sure to put the CDF file in your annotationData/chipTypes/XX/ where
>> >> XX is the platform you are using (e.g. HuGene-1_0-st-v1 for Human
>> >> Gene 1.0 ST, HT_HG-U133_Plus_PM for the human PM plate arrays, etc.)
>> >>
>> >> On Tue, Aug 3, 2010 at 2:27 PM, vish <ashwin4bioinformat...@gmail.com>
>> >> wrote:
>> >> >
>> >> > I am really new to this aroma.affymetrix. I am trying to analyze
>> >> > HuGene-1_0-st-v1 array and interested in Quality control check/
>> >> > Assessment.
>> >> > when I am trying to run this command I am ending up with this error .
>> >> > Any help is greatly appreciated.
>> >> >
>> >> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
>> >> > Error in list(`AffymetrixCdfFile$byChipType(chipType, tags = "r3")` =
>> >> > <environment>, :
>> >> >
>> >> > [2010-08-03 16:23:44] Exception: Could not locate a file for this
>> chip
>> >> > type: HuGene-1_0-st-v1,r3
>> >> > at throw(Exception(...))
>> >> > at throw.default("Could not locate a file for this chip type: ",
>> >> > paste(c(chipType, tags), collapse = ","))
>> >> > at throw("Could not locate a file for this chip type: ",
>> >> > paste(c(chipType, tags), collapse = ","))
>> >> > at method(static, ...)
>> >> > at AffymetrixCdfFile$byChipType(chipType, tags = "r3")
>> >> >
>> >> > Ashwin
>> >> >
>> >> > --
>> >> > 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
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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
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>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> > To unsubscribe and other options, go to
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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
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>> To post to this group, send email to aroma-affymetrix@googlegroups.com
>> To unsubscribe and other options, go to
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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
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