On Wed, Nov 30, 2011 at 2:12 PM, Henrik Bengtsson
<henrik.bengts...@aroma-project.org> wrote:
> Hi.
>
> NO REPLY EXPECTED
The above sentence was a mistake - seems to been added by my email
client. Feel free to reply. /H
>
>
> On Wed, Nov 30, 2011 at 12:24 AM, Peiyong <jiangpeiy...@cuhk.edu.hk> wrote:
>> Thanks!
>>
>> directory structure:
>> /A/B/C/
>> |-- annotationData
>> | `-- chipTypes
>> | `-- GenomeWideSNP_6
>> | |-- GenomeWideSNP_6,Full.acs
>> | |-- GenomeWideSNP_6,Full.ufc
>> | |-- GenomeWideSNP_6,Full.ufl
>> | |-- GenomeWideSNP_6,Full.ugp
>> | `-- GenomeWideSNP_6.cdf
>
> Not correct, because the CDF is the "default" CDF, whereas the other
> annotation files are for the "full" CDF (at least their tags claim
> that - more below).
>
>>
>> `-- rawData
>> `-- run1
>> `-- GenomeWideSNP_6
>> |-- test1,GenomeWideSNP_6.CEL
>> `-- test2,GenomeWideSNP_6.CEL
>
> Correct.
>
>>
>> R scripts:
>> setwd("/A/B/C/")
>> cdf <- AffymetrixCdfFile$byChipType(chipType='GenomeWideSNP_6');
>> #ugp <- AromaUgpFile$allocateFromCdf(cdf, tag='Full');
>> #acs <- AromaCellSequenceFile$allocateFromCdf(cdf, tag='Full');
>> #Ufl <- AromaUflFile$allocateFromCdf(cdf, tag='Full');
>> #ufc <- AromaUfcFile$allocateFromCdf(cdf, tag='Full');
>
> Those 4 commented lines *allocates* empty annotation files based on
> the mapping of the (default) CDF (but with tags "full"). Anyway, you
> don't want to do this. They are all empty and contains no annotation
> information (which is why you get the error below). Instead you want
> to download them from:
>
> http://aroma-project.org/chipTypes/GenomeWideSNP_6/
>
> Make sure to get the "Full" ones if you use the "Full" CDF, otherwise
> the ones without the "Full" tag. That page also explains what
> "default" and "full" means (which only applies to GenomeWideSNP_5 and
> GenomeWideSNP_6).
>
> /Henrik
>
>>
>> csR=AffymetrixCelSet$byName('run1', chipType='GenomeWideSNP_6')
>> pair <- c(T="test1", N="test2")
>> csR <- extract(csR, indexOf(csR, pair))
>> ds <- doCRMAv2(csR, chipType="GenomeWideSNP_6", verbose=-10)
>>
>> traceback() show that:
>>
>> 12: stop(paste(ch, " is not ", if (length(r) > 1L) "all ", "TRUE",
>> sep = ""), call. = FALSE)
>> 11: stopifnot(length(uPos) > 0)
>> 10: getSnpNucleotides.AromaCellSequenceFile(this, cells = cells,
>> ..., verbose = verbose)
>> 9: getSnpNucleotides(this, cells = cells, ..., verbose = verbose)
>> 8: groupBySnpNucleotides.AromaCellSequenceFile(acs, cells = cells,
>> shifts = shifts, verbose = verbose)
>> 7: groupBySnpNucleotides(acs, cells = cells, shifts = shifts, verbose =
>> verbose)
>> 6: getSetsOfProbes.AllelicCrosstalkCalibration(this, verbose =
>> less(verbose,
>> 1))
>> 5: getSetsOfProbes(this, verbose = less(verbose, 1))
>> 4: process.AllelicCrosstalkCalibration(acc, verbose = verbose)
>> 3: process(acc, verbose = verbose)
>> 2: doCRMAv2.AffymetrixCelSet(csR, chipType = "GenomeWideSNP_6",
>> verbose = -10)
>> 1: doCRMAv2(csR, chipType = "GenomeWideSNP_6", verbose = -10)
>>
>> And ds <- doCRMAv2(csR, chipType="GenomeWideSNP_6", verbose=-10) shows
>> ...........
>> Checking for cached results...done
>> Identifying SNP positions of cell allele pairs...done
>> SNP positions:
>> int [1:2850731] NA NA NA NA NA NA NA NA NA NA ...
>> Tabulated SNP positions:
>> character(0)
>> Unique SNP positions:
>> integer(0)
>> Error: length(uPos) > 0 is not TRUE
>> Retrieving SNP nucleotides...done
>> Get SNP nucleotide sequence pairs...done
>> Identifying groups of SNP nucleotide sequence pairs...done
>> Non-SNP units:...done
>> Identifying cell indices for all non-SNP units...done
>> Identifying sets of pairs of cell indices...done
>> Array #1 ('test1') of 2...done
>> Calibrating 2 arrays...done
>> Calibrating data set for allelic cross talk...done
>>
>> Then the sessionInfo() shows
>>
>> R version 2.14.0 (2011-10-31)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
>> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
>> [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
>> [7] LC_PAPER=C LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] aroma.affymetrix_2.3.0 affxparser_1.26.2 aroma.apd_0.2.0
>> [4] R.huge_0.3.0 aroma.core_2.3.2 aroma.light_1.22.0
>> [7] matrixStats_0.4.0 R.rsp_0.7.0 R.cache_0.5.2
>> [10] R.filesets_1.1.3 digest_0.5.1 R.utils_1.9.6
>> [13] R.oo_1.8.3 R.methodsS3_1.2.1 limma_3.10.0
>> [16] affy_1.32.0 Biobase_2.14.0
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.22.0 BiocInstaller_1.2.1 preprocessCore_1.16.0
>> [4] tools_2.14.0 zlibbioc_1.0.0
>>
>>
>> On Wed, Nov 30, 2011 at 4:05 PM, Henrik Bengtsson
>> <henrik.bengts...@aroma-project.org> wrote:
>>>
>>> Congratulations - you just won the price for the world shortest issue
>>> report ;)
>>>
>>> Some ideas:
>>>
>>> 1. Use argument verbose=-10
>>> 2. Use traceback() when you get an error.
>>>
>>> Other than that:
>>>
>>> 3. What is your sessionInfo()?
>>> 4. Show us your script.
>>>
>>> /Henrik
>>>
>>> On Tue, Nov 29, 2011 at 11:57 PM, Peiyong <wanna...@gmail.com> wrote:
>>> > How to figure following issue when run doASCRMAv2()
>>> >
>>> > Error: length(uPos) > 0 is not TRUE
>>> >
>>> > --
>>> > 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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>>>
>>> --
>>> 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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>>
>>
>>
>>
>> --
>> Jiang Peiyong
>>
>> --
>> 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/
