Re: [aroma.affymetrix] Re: Error in "getGenomeInformation"
On Wed, Jun 27, 2012 at 9:09 AM, Andrew wrote:
> thanks Henrik.
>
> The output is:
>
> [1] "GenomeWideSNP_6,Full.cdf"
> [2] "GenomeWideSNP_6,HB20080710.acs"
> [3] "GenomeWideSNP_6,na31,hg19,HB20110328.ufl"
> [4] "GenomeWideSNP_6,na31,hg19,HB20110328.ugp"
For "GenomeWideSNP_6,Full.cdf", you need (=missing):
"GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl"
"GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp"
For "GenomeWideSNP_6.cdf", you need/have:
"GenomeWideSNP_6,na31,hg19,HB20110328.ufl"
"GenomeWideSNP_6,na31,hg19,HB20110328.ugp"
"GenomeWideSNP_6,HB20080710.acs" is the same for both CDFs.
/Henrik
>
>
>
> On Tuesday, June 26, 2012 11:51:49 PM UTC-4, Henrik Bengtsson wrote:
>>
>> Following the troubleshooting of annotationData/ on
>> http://aroma-project.org/troubleshooting/DirectoryStructures using
>> chipType <- "GenomeWideSNP_6", what does print(list.files(path=path))
>> output?
>>
>> /Henrik
>>
>> On Tue, Jun 26, 2012 at 8:04 PM, Andrew wrote:
>> > I feel it might be better to post my question in this thread, as I have
>> > encountered the same error.
>> >
>> > I've downloaded ufl, ugp, and acs files from AROMA SNP6 webpage, and the
>> > Full cdf file from Affymetrix. And I still got the same kind error
>> > NT_CMU
>> > got for "getGenomeInformation".
>> >
>> > Could you please give me a hint, where should I look for? Thanks!
>> >
>> >
>> > On Monday, June 18, 2012 4:58:19 PM UTC-4, NT_CMU wrote:
>> >>
>> >> Hi
>> >>
>> >> I'm trying to run the command "doCRMAv2", and i get these errors. Let
>> >> me
>> >> know what the problem is, if any of you have encountered this before. I
>> >> thought i did not have some library installed but, i have both ACNE and
>> >> aroma.affymetrix working properly.
>> >>
>> >> > ds <- doCRMAv2("LeeAV_2012",chipType="GenomeWideSNP_6,Full")
>> >> Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
>> >> [2012-06-18 16:55:10] Exception: Failed to retrieve genome information
>> >> for
>> >> this chip type: GenomeWideSNP_6
>> >>
>> >> at #12. getGenomeInformation.AffymetrixCdfFile(cdf)
>> >> - getGenomeInformation.AffymetrixCdfFile() is in environment
>> >> 'aroma.affymetrix'
>> >>
>> >> at #11. getGenomeInformation(cdf)
>> >> - getGenomeInformation() is in environment 'aroma.affymetrix'
>> >>
>> >> at #10. getSubsetToAvg.AllelicCrosstalkCalibration(this)
>> >> - getSubsetToAvg.AllelicCrosstalkCalibration() is in
>> >> environment
>> >> 'aroma.affymetrix'
>> >>
>> >> at #09. getSubsetToAvg(this)
>> >> - getSubsetToAvg() is in environment 'aroma.affymetrix'
>> >>
>> >> at #08. getParameters.AllelicCrosstalkCalibration(this)
>> >> - getParameters.AllelicCrosstalkCalibration() is in
>> >> environment
>> >> 'aroma.affymetrix'
>> >>
>> >> at #07. getParameters(this)
>> >> - getParameters() is in environment 'R.rsp'
>> >>
>> >> at #06. process.AllelicCrosstalkCalibration(acc, verbose = verbose)
>> >> - process.AllelicCrosstalkCalibration() is in environment
>> >>
>> >>
>> >> Thanks
>> >>
>> >> Nitesh
>> >
>> > --
>> > 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
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Re: [aroma.affymetrix] Re: Error in "getGenomeInformation"
thanks Henrik.
The output is:
[1] "GenomeWideSNP_6,Full.cdf"
[2] "GenomeWideSNP_6,HB20080710.acs"
[3] "GenomeWideSNP_6,na31,hg19,HB20110328.ufl"
[4] "GenomeWideSNP_6,na31,hg19,HB20110328.ugp"
On Tuesday, June 26, 2012 11:51:49 PM UTC-4, Henrik Bengtsson wrote:
>
> Following the troubleshooting of annotationData/ on
> http://aroma-project.org/troubleshooting/DirectoryStructures using
> chipType <- "GenomeWideSNP_6", what does print(list.files(path=path))
> output?
>
> /Henrik
>
> On Tue, Jun 26, 2012 at 8:04 PM, Andrew wrote:
> > I feel it might be better to post my question in this thread, as I have
> > encountered the same error.
> >
> > I've downloaded ufl, ugp, and acs files from AROMA SNP6 webpage, and the
> > Full cdf file from Affymetrix. And I still got the same kind error
> NT_CMU
> > got for "getGenomeInformation".
> >
> > Could you please give me a hint, where should I look for? Thanks!
> >
> >
> > On Monday, June 18, 2012 4:58:19 PM UTC-4, NT_CMU wrote:
> >>
> >> Hi
> >>
> >> I'm trying to run the command "doCRMAv2", and i get these errors. Let
> me
> >> know what the problem is, if any of you have encountered this before. I
> >> thought i did not have some library installed but, i have both ACNE and
> >> aroma.affymetrix working properly.
> >>
> >> > ds <- doCRMAv2("LeeAV_2012",chipType="GenomeWideSNP_6,Full")
> >> Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
> >> [2012-06-18 16:55:10] Exception: Failed to retrieve genome information
> for
> >> this chip type: GenomeWideSNP_6
> >>
> >> at #12. getGenomeInformation.AffymetrixCdfFile(cdf)
> >> - getGenomeInformation.AffymetrixCdfFile() is in environment
> >> 'aroma.affymetrix'
> >>
> >> at #11. getGenomeInformation(cdf)
> >> - getGenomeInformation() is in environment 'aroma.affymetrix'
> >>
> >> at #10. getSubsetToAvg.AllelicCrosstalkCalibration(this)
> >> - getSubsetToAvg.AllelicCrosstalkCalibration() is in
> environment
> >> 'aroma.affymetrix'
> >>
> >> at #09. getSubsetToAvg(this)
> >> - getSubsetToAvg() is in environment 'aroma.affymetrix'
> >>
> >> at #08. getParameters.AllelicCrosstalkCalibration(this)
> >> - getParameters.AllelicCrosstalkCalibration() is in
> environment
> >> 'aroma.affymetrix'
> >>
> >> at #07. getParameters(this)
> >> - getParameters() is in environment 'R.rsp'
> >>
> >> at #06. process.AllelicCrosstalkCalibration(acc, verbose = verbose)
> >> - process.AllelicCrosstalkCalibration() is in environment
> >>
> >>
> >> Thanks
> >>
> >> Nitesh
> >
> > --
> > 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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Re: [aroma.affymetrix] Re: Error in "getGenomeInformation"
Following the troubleshooting of annotationData/ on
http://aroma-project.org/troubleshooting/DirectoryStructures using
chipType <- "GenomeWideSNP_6", what does print(list.files(path=path))
output?
/Henrik
On Tue, Jun 26, 2012 at 8:04 PM, Andrew wrote:
> I feel it might be better to post my question in this thread, as I have
> encountered the same error.
>
> I've downloaded ufl, ugp, and acs files from AROMA SNP6 webpage, and the
> Full cdf file from Affymetrix. And I still got the same kind error NT_CMU
> got for "getGenomeInformation".
>
> Could you please give me a hint, where should I look for? Thanks!
>
>
> On Monday, June 18, 2012 4:58:19 PM UTC-4, NT_CMU wrote:
>>
>> Hi
>>
>> I'm trying to run the command "doCRMAv2", and i get these errors. Let me
>> know what the problem is, if any of you have encountered this before. I
>> thought i did not have some library installed but, i have both ACNE and
>> aroma.affymetrix working properly.
>>
>> > ds <- doCRMAv2("LeeAV_2012",chipType="GenomeWideSNP_6,Full")
>> Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
>> [2012-06-18 16:55:10] Exception: Failed to retrieve genome information for
>> this chip type: GenomeWideSNP_6
>>
>> at #12. getGenomeInformation.AffymetrixCdfFile(cdf)
>> - getGenomeInformation.AffymetrixCdfFile() is in environment
>> 'aroma.affymetrix'
>>
>> at #11. getGenomeInformation(cdf)
>> - getGenomeInformation() is in environment 'aroma.affymetrix'
>>
>> at #10. getSubsetToAvg.AllelicCrosstalkCalibration(this)
>> - getSubsetToAvg.AllelicCrosstalkCalibration() is in environment
>> 'aroma.affymetrix'
>>
>> at #09. getSubsetToAvg(this)
>> - getSubsetToAvg() is in environment 'aroma.affymetrix'
>>
>> at #08. getParameters.AllelicCrosstalkCalibration(this)
>> - getParameters.AllelicCrosstalkCalibration() is in environment
>> 'aroma.affymetrix'
>>
>> at #07. getParameters(this)
>> - getParameters() is in environment 'R.rsp'
>>
>> at #06. process.AllelicCrosstalkCalibration(acc, verbose = verbose)
>> - process.AllelicCrosstalkCalibration() is in environment
>>
>>
>> Thanks
>>
>> Nitesh
>
> --
> 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/
Re: [aroma.affymetrix] Re: Error in "getGenomeInformation"
You can ignore them. Warnings are almost always alright - errors are not.
/Henrik
On Tue, Jun 19, 2012 at 6:40 AM, NT_CMU wrote:
> Thank you Henrik and Pierre. I am able to run it successfully now.
>
> It gives me a few warnings at the end.
>
>> warnings()
> Warning messages:
> 1: In log2(y) : NaNs produced
> 2: In log2(y) : NaNs produced
> 3: In log2(y) : NaNs produced
> 4: In log2(y) : NaNs produced
> 5: In log2(y) : NaNs produced
> 6: In log2(y) : NaNs produced
> 7: In log2(y) : NaNs produced
> 8: In log2(y) : NaNs produced
> 9: In log2(y) : NaNs produced
> 10: In log2(y) : NaNs produced
> 11: In log2(y) : NaNs produced
> 12: In log2(y) : NaNs produced
> 13: In log2(y) : NaNs produced
> 14: In log2(y) : NaNs produced
> 15: In log2(y) : NaNs produced
> 16: In log2(y) : NaNs produced
> 17: In log2(y) : NaNs produced
> 18: In log2(y) : NaNs produced
> 19: In log2(y) : NaNs produced
> 20: In log2(y) : NaNs produced
> 21: In log2(y) : NaNs produced
> 22: In log2(y) : NaNs produced
> 23: In log2(y) : NaNs produced
> 24: In log2(y) : NaNs produced
>
>
> Any suggestions as to how to avoid them and what they mean with respect to
> doCRMAv2 ?
>
> Thanks
>
> Nitesh
>
> On Monday, 18 June 2012 16:58:19 UTC-4, NT_CMU wrote:
>>
>> Hi
>>
>> I'm trying to run the command "doCRMAv2", and i get these errors. Let me
>> know what the problem is, if any of you have encountered this before. I
>> thought i did not have some library installed but, i have both ACNE and
>> aroma.affymetrix working properly.
>>
>> > ds <- doCRMAv2("LeeAV_2012",chipType="GenomeWideSNP_6,Full")
>> Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
>> [2012-06-18 16:55:10] Exception: Failed to retrieve genome information for
>> this chip type: GenomeWideSNP_6
>>
>> at #12. getGenomeInformation.AffymetrixCdfFile(cdf)
>> - getGenomeInformation.AffymetrixCdfFile() is in environment
>> 'aroma.affymetrix'
>>
>> at #11. getGenomeInformation(cdf)
>> - getGenomeInformation() is in environment 'aroma.affymetrix'
>>
>> at #10. getSubsetToAvg.AllelicCrosstalkCalibration(this)
>> - getSubsetToAvg.AllelicCrosstalkCalibration() is in environment
>> 'aroma.affymetrix'
>>
>> at #09. getSubsetToAvg(this)
>> - getSubsetToAvg() is in environment 'aroma.affymetrix'
>>
>> at #08. getParameters.AllelicCrosstalkCalibration(this)
>> - getParameters.AllelicCrosstalkCalibration() is in environment
>> 'aroma.affymetrix'
>>
>> at #07. getParameters(this)
>> - getParameters() is in environment 'R.rsp'
>>
>> at #06. process.AllelicCrosstalkCalibration(acc, verbose = verbose)
>> - process.AllelicCrosstalkCalibration() is in environment
>>
>>
>> Thanks
>>
>> Nitesh
>
> --
> 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/
