Hi Mark,
Thanks for making our code available, its a great help. I have an
error reproducing part of it which is bothering me.
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/HuEx-1_0-st-v2
Filename: HuEx-1_0-st-v2,mainR3,A20071112,EP.cdf
Filesize: 207.11MB
Chip type: HuEx-1_0-st-v2,mainR3,A20071112,EP
RAM: 10.76MB
File format: v4 (binary; XDA)
Dimension: 2560x2560
Number of cells: 6553600
Number of units: 312355
Cells per unit: 20.98
Number of QC units: 1
> u <- indexOf(cdf,"3400034")
> ugcM <- getUnitGroupCellMap(getCdf(ds), units=u, retNames=TRUE)
> ind <-
> getCellIndices(cdf,units=ugcM$cell,verbose=verbose,useNames=FALSE,unlist=TRUE)
Reading cell indices from CDF file...
Pathname: annotationData/chipTypes/HuEx-1_0-st-v2/HuEx-1_0-st-
v2,mainR3,A20071112,EP.cdf
Units:
int [1:580] 492971 1601392 2403106 1266048 4113396 2553742 4778669
393366 4077660 5416469 ...
lapplyInChunks()...
Number of elements per chunk: 1e+05
Chunk #1 of 1...
Elements:
int [1:580] 492971 1601392 2403106 1266048 4113396 2553742 4778669
393366 4077660 5416469 ...
Querying CDF file...
Error in readCdfCellIndices(pathname, ...) :
Argument 'units' contains an element out of range: 492971
Querying CDF file...done
Chunk #1 of 1...done
lapplyInChunks()...done
Reading cell indices from CDF file...done
Why is cell 492971 out of range? Any insight appreciated.
I am using windows:
> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32
locale:
LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New Zealand.
1252;LC_MONETARY=English_New Zealand.
1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252
attached base packages:
[1] grid stats graphics grDevices utils datasets
methods base
other attached packages:
[1] GenomeGraphs_1.4.1 biomaRt_2.0.0
aroma.affymetrix_1.1.0 aroma.apd_0.1.3 R.huge_0.1.7
affxparser_1.16.0
[7] aroma.core_1.1.0 aroma.light_1.13.2
matrixStats_0.1.5 R.rsp_0.3.4 R.filesets_0.5.1
digest_0.3.1
[13] R.cache_0.1.7 R.utils_1.1.6
R.oo_1.4.6 R.methodsS3_1.0.3
loaded via a namespace (and not attached):
[1] RCurl_0.98-1 XML_2.5-1
BTW (for fellow windows sufferers)
The way I generated the small probeset file was with a perl script
(one free implementation is with Activestate perl and UnxUtils). Here
is the script:
#!C:/Perl/bin/perl
while(<>){
next if(/^#/);
chomp;
s/"//g;
@sl = split(/,/,$_);
for $i ( 0..7) {print $sl[$i],",";}
print $sl[8],"\n";
}
save it to foo.pl then (say using the unix.sh from UnxUtils) go
perl foo.pl HuEx-1_0-st-v2.na28.hg18.probeset.csv
regards,
John
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