Re: [aroma.affymetrix] Re: Could not locate a file for this chip type: Mapping50K_Hind240 (Was: FW:)

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Re: [aroma.affymetrix] Re: Could not locate a file for this chip type: Mapping50K_Hind240 (Was: FW:)

Henrik Bengtsson-2
Hi.

On Thu, Nov 18, 2010 at 9:40 AM, Yan Jiao <[hidden email]> wrote:

>
> Dear all,
>
> I’m trying to solve  my copynumber segmentation problem using aroma
> affymetrix, according to the Vignette
>
> I created a folder : rawData ,under my working directory, and inside that
> folder I created another folder Mapping50K_Hind240 , inside which I put my
> 600ish .cel file
>
> Isn’t it correct?

No.  You missed that you need a data set directory to under rawData,
e.g. rawData/NameOfMyDataSet/Mapping50K_Hind240/.  See for instance
page 'Setup: Quick Summary Of Required File Structure'
[http://aroma-project.org/node/79].  See also
http://aroma-project.org/setup/.

>
>
>
> Then I did :
>
>
>
> ds <- doCRMAv1("R:/work/breast/breast data files/MYC/rawData",
> chipType="Mapping50K_Hind240")

You should never have to specify a path/directory when using the aroma
framework, instead it should look something like:

ds <- doCRMAv1("NameOfMyDataSet", chipType="Mapping50K_Hind240");

Since the aroma framework nows where to look for data files, it is all
automagically taken care of.

Hope this helps

Henrik

>
>
>
> (“R:/work/breast/breast data files/MYC/” is my working directory)
>
>
>
> Why I got the error message:
>
>
>
> Error in list(`doCRMAv1("R:/work/breast/breast data files/MYC/rawData",
> chipType = "Mapping50K_Hind240")` = <environment>,  :
>
>
>
> [2010-11-18 16:41:10] Exception: Could not locate a file for this chip type:
> Mapping50K_Hind240
>
>   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$byChipType(chipType)
>
>   at method(static, ...)
>
>   at AffymetrixCelSet$byName(dataSet, ..., verbose = less(verbose, 50),
> .onUnknownArgs = "ignore")
>
>   at doCRMAv1.character("R:/work/breast/breast data files/MYC/rawData",
> chipType = "Mapping50K_Hind240")
>
>   at doCRMAv1("R:/work/breast/breast data files/MYC/rawData", chipType =
> "Mapping50K_Hind240")
>
>
>
>
>
>
>
>
>
> could anyone enlighten me please?
>
>
>
>
>
> Many thanks
>
>
>
> **********************************************************************
>
> This email and any files transmitted with it are confidential and
>
> intended solely for the use of the individual or entity to whom they
>
> are addressed. If you have received this email in error please notify
>
> the system manager ([hidden email]).
>
> **********************************************************************
>
>
>
> --
> 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 [hidden email]
> 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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Re: [aroma.affymetrix] Re: Could not locate a file for this chip type: Mapping50K_Hind240 (Was: FW:)

Henrik Bengtsson-2
Hi again,

On Fri, Nov 19, 2010 at 10:35 AM, Henrik Bengtsson
<[hidden email]> wrote:

> Hi.
>
> On Thu, Nov 18, 2010 at 9:40 AM, Yan Jiao <[hidden email]> wrote:
>>
>> Dear all,
>>
>> I’m trying to solve  my copynumber segmentation problem using aroma
>> affymetrix, according to the Vignette
>>
>> I created a folder : rawData ,under my working directory, and inside that
>> folder I created another folder Mapping50K_Hind240 , inside which I put my
>> 600ish .cel file
>>
>> Isn’t it correct?
>
> No.  You missed that you need a data set directory to under rawData,
> e.g. rawData/NameOfMyDataSet/Mapping50K_Hind240/.  See for instance
> page 'Setup: Quick Summary Of Required File Structure'
> [http://aroma-project.org/node/79].  See also
> http://aroma-project.org/setup/.

Actually, although that was also an error, the error message reported
on is that it cannot locate the annotation data file.  Again, see the
above two URLs; you need to setup
annotationData/chipTypes/Mapping50K_Hind240/ so it contains the
correct CDF file etc.  You need to download the CDF file from the
Affymetrix website, cf. http://aroma-project.org/faq/

/Henrik

>
>>
>>
>>
>> Then I did :
>>
>>
>>
>> ds <- doCRMAv1("R:/work/breast/breast data files/MYC/rawData",
>> chipType="Mapping50K_Hind240")
>
> You should never have to specify a path/directory when using the aroma
> framework, instead it should look something like:
>
> ds <- doCRMAv1("NameOfMyDataSet", chipType="Mapping50K_Hind240");
>
> Since the aroma framework nows where to look for data files, it is all
> automagically taken care of.
>
> Hope this helps
>
> Henrik
>
>>
>>
>>
>> (“R:/work/breast/breast data files/MYC/” is my working directory)
>>
>>
>>
>> Why I got the error message:
>>
>>
>>
>> Error in list(`doCRMAv1("R:/work/breast/breast data files/MYC/rawData",
>> chipType = "Mapping50K_Hind240")` = <environment>,  :
>>
>>
>>
>> [2010-11-18 16:41:10] Exception: Could not locate a file for this chip type:
>> Mapping50K_Hind240
>>
>>   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$byChipType(chipType)
>>
>>   at method(static, ...)
>>
>>   at AffymetrixCelSet$byName(dataSet, ..., verbose = less(verbose, 50),
>> .onUnknownArgs = "ignore")
>>
>>   at doCRMAv1.character("R:/work/breast/breast data files/MYC/rawData",
>> chipType = "Mapping50K_Hind240")
>>
>>   at doCRMAv1("R:/work/breast/breast data files/MYC/rawData", chipType =
>> "Mapping50K_Hind240")
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> could anyone enlighten me please?
>>
>>
>>
>>
>>
>> Many thanks
>>
>>
>>
>> **********************************************************************
>>
>> This email and any files transmitted with it are confidential and
>>
>> intended solely for the use of the individual or entity to whom they
>>
>> are addressed. If you have received this email in error please notify
>>
>> the system manager ([hidden email]).
>>
>> **********************************************************************
>>
>>
>>
>> --
>> 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 [hidden email]
>> 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 [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/