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
`-- rawData
`-- run1
`-- GenomeWideSNP_6
|-- test1,GenomeWideSNP_6.CEL
`-- test2,GenomeWideSNP_6.CEL
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$allocateFromCdf(cdf, tag='Full');
csR=AffymetrixCelSet$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
> 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/
>
--
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/
