Hi,
I'm encountering two errors:
1) error happens with:
cs <- AffymetrixCelSet$byName(dataSet, cdf=cdf);
print(cs)
Error in if (hasTimestamp) { : argument is of length zero
It seems that samples that go through have:
getHeader(getFile(cs, 1))$datheader
[1] "[0..65534] D1_GenomeWideSNP_6:CLS=20508RWS=20508XIN=0 YIN=0
VE=0 0 12/10/10 12:05:43 50205130 M10 \024 \024
GenomeWideSNP_6.1sq \024 \024 \024 \024 \024 570 \024 25565.199219
\024 3.500000 \024 0.7000 \024 3"
And samples that don't go through have something like:
getHeader(getFile(cs, 5))$datheader
[1] "[2..65534]
D2_plus_D1785_GenomeWideSNP_6:CLS=20491RWS=20491XIN=0 YIN=0
VE=0 0 12/09/10 01:52:21 50205130 M10 \024 \024 .1sq
\024 \024 \024 \024 \024 570 \024 25556.708984 \024 3.500000 \024
0.7000 \024 3"
If I get rid of samples that have .1sq instead of GenomeWideSNP_6.1sq,
everything works
2)
then I encounter the second problem with process(acc,
verbose=verbose), reported by DGoode as well
Error: length(pos) == ncol(cells) is not TRUE
csC <- process(acc, verbose=verbose);
Calibrating data set for allelic cross talk...
Compressing model parameter to a short format...
Compressing model parameter to a short format...done
Calibrating 61 arrays...
Path: probeData/data,ACC,ra,-XY/GenomeWideSNP_6
Array #1 ('DC_D1123_GenomeWideSNP_6') of 61...
Identifying sets of pairs of cell indices...
Chip type: GenomeWideSNP_6,Full
Merge shifts: TRUE
Number of nucleotides: 1
Locating AromaCellSequenceFile...
Chip type: GenomeWideSNP_6
Number of cells: 6892960
AromaCellSequenceFile:
Name: GenomeWideSNP_6
Tags: HB20080710
Full name: GenomeWideSNP_6,HB20080710
Pathname: annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,HB20080710.acs
File size: 170.92 MB (179217531 bytes)
RAM: 0.00 MB
Number of data rows: 6892960
File format: v1
Dimensions: 6892960x26
Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw,
raw, raw
Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
Footer: <createdOn>20080710 22:47:02 PDT</
createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</
chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</
filename><filesize>341479928</
filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></
srcFile><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</
filename><filesize>96968290</
filesize><checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></
srcFile2>
Chip type: GenomeWideSNP_6
Platform: Affymetrix
Locating AromaCellSequenceFile...done
Identifying cell indices for all non-SNP units...
Non-SNP units:...
int [1:946447] 1 2 3 4 5 6 7 8 9 10 ...
Reading cell indices from CDF file...
Pathname: annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full.cdf
Units:
int [1:946447] 1 2 3 4 5 6 7 8 9 10 ...
lapplyInChunks()...
Number of elements per chunk: 1e+05
Chunk #1 of 10...
...
Identifying SNP positions of cell allele pairs...
Checking for cached results...
Found cached results
Checking for cached results...done
Identifying SNP positions of cell allele pairs...done
SNP positions:
int [1:2916605] 10 10 10 11 11 11 11 11 11 16 ...
Error: length(pos) == ncol(cells) 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 ('DC_D1123_GenomeWideSNP_6') of 61...done
Calibrating 61 arrays...done
Calibrating data set for allelic cross talk...done
> print(csC);
Error in print(csC) : object 'csC' not found
sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] ACNE_0.4.3 MASS_7.3-13
aroma.affymetrix_2.1.6
[4] affxparser_1.24.0 aroma.apd_0.2.0 R.huge_0.3.0
[7] aroma.core_2.1.4 aroma.light_1.20.0 matrixStats_0.2.2
[10] R.rsp_0.6.2 R.cache_0.4.3 R.filesets_1.1.0
[13] digest_0.5.0 R.utils_1.7.8 R.oo_1.8.1
[16] R.methodsS3_1.2.1
Any recommendations?
Thanks!
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