Just to close this (old) thread:
On Mon, May 7, 2012 at 1:07 PM, sean nj <njs...@gmail.com> wrote:
> Hi guys,
>
> I tried to convert recent customCDF HTHGU133A_Hs_ENTREZG.cdf (version 15.10)
> to binary format and end up with error message:
>
> Error in convertCdf("HTHGU133A_Hs_ENTREZG.cdf",
> "HTHGU133A_Hs_ENTREZG,Binary.cdf", :
> An inconsistency between source and destination CDF was detected.
> Reason:Units:
> Any suggestion?
This happened because:
1. That ASCII CDF (HTHGU133A_Hs_ENTREZG.cdf) from BrainArray
[http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/15.1.0/entrezg.asp]
claims there are 12,074 units (NumberOfUnits=12074), but there are
really only 12,073 units. This is related to thread 'convertCdf()
crashes R while converting BrainArray custom CDF for Affy
HT_HG-U133_Plus_PM' on July 3, 2011 [http://goo.gl/QgRsW].
2. Because of the above, convertCdf() will read that false extra unit
as an empty unit that has an 'unknown' unit type.
3. In affxparser (<= 1.30.1), an 'unknown' unit type was incorrectly
encoded by convertCdf() making the unit type appear as a 'copynumber'
unit. This difference is what is detected in the 'Comparing CDFs'
step below.
It's not a serious problem that the unit type is incorrect for this
false extra unit, because it is empty (no groups and no probes)
anyway.
FYI, the encoding error in convertCdf() has been fixed in affxparser
v1.30.2 (just submitted to Bioconductor).
Case closed
/Henrik
>
> Thanks,
>
> Ying
>
>> library(affxparser)
>> convertCdf("HTHGU133A_Hs_ENTREZG.cdf","HTHGU133A_Hs_ENTREZG,Binary.cdf",
> + version = 4,force = TRUE,verbose=TRUE)
> Reading CDF header...
> Reading CDF header...done
> Reading CDF QC units...
> Reading CDF QC units...done
> Reading CDF units...
> Reading CDF units...done
> Writing CDF structure...
> Timing for writeCdf():
> user system elapsed
> 10.11 0.02 10.14
> Writing CDF structure...done
> Comparing CDFs...
> Comparing CDFs...
> CDF 1: ./HTHGU133A_Hs_ENTREZG.cdf
> CDF 2: ./HTHGU133A_Hs_ENTREZG,Binary.cdf
> Comparing CDF headers...
> Comparing CDF headers...done
> Comparing QC units...
> Comparing QC units...done
> Comparing units...
> Error in convertCdf("HTHGU133A_Hs_ENTREZG.cdf",
> "HTHGU133A_Hs_ENTREZG,Binary.cdf", :
> An inconsistency between source and destination CDF was detected.
> Reason:Units:
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
> locale:
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> other attached packages:
> [1] affxparser_1.28.0 BiocInstaller_1.4.4
> loaded via a namespace (and not attached):
> [1] tools_2.15.0
>>
>
>
> --
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--
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