See if the new troubleshooting page 'Setup of directory structures':
http://aroma-project.org/troubleshooting/DirectoryStructures
will help you.
/Henrik
On Thu, Aug 5, 2010 at 8:47 PM, ashwin Vishnuvardhana
<ashwin4bioinformat...@gmail.com> wrote:
> 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
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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
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>>> >> To post to this group, send email to aroma-affymetrix@googlegroups.com
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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
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>>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
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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
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