Hi.
On Tue, May 22, 2012 at 3:41 AM, Cristian Bassi
<[email protected]> wrote:
> Hi everyone,
> I successfully applied CRMAv2 for estimating copy numbers from a set of 14
> paired samples, and after the segmentation process I used chromosome
> explorer for displaying the results.
> The problem is that the regions positions listed in regions.xls file are all
> shifted forward 13 nucleotides, compared to the genomic locations of the
> probes provided by Affymetrix (i checked only CN probes....but also SNPs
> probes are shifted forward some nucleotide..). Does anyone knows how to
> solve this ?
So, I think there is nothing that have to be solved, because from
AFFX_README-NetAffx-CN-CSV-Files.txt (in e.g.
GenomeWideSNP_6.cn.na31.annot.csv.zip from Affymetrix) one can read
that its (start, stop) positions are defined as:
3. Chromosome Start: The start base position of the 5'-most probe in
the probe set.
4. Chromosome Stop: The end base position of the 3'-most probe in
the probe set.
and in the position in the UGP file is defined as Start+13bp where
offset 13 is representing the middle nucleotide of 25 mers.
DETAILS: The offset/shift of 13 is given by argument 'shift' of
importFromAffymetrixNetAffxCsvFile() for AromaUgpFile, e.g.
> args(importFromAffymetrixNetAffxCsvFile.AromaUgpFile)
function (this, csv, shift = "auto", onReplicates = c("median",
"mean", "overwrite"), ..., verbose = FALSE)
Peaking inside that function, one can see that shift == "auto" becomes
shift=+13L.
>
> I created new UGP, UFL and ACS files following this guides:
> - for UGP: http://www.aroma-project.org/node/43 (importing from NetAffx
> files) and using the newest affymetrix files:
> GenomeWideSNP_6.na32.annot.csv, GenomeWideSNP_6.cn.na32.annot.csv.zip;
UGP contains only (chromosome, position).
> - for UFL: http://www.aroma-project.org/node/47 (importing from NetAffx
> files) and using the newest affymetrix files:
> GenomeWideSNP_6.na32.annot.csv, GenomeWideSNP_6.cn.na32.annot.csv.zip;
UFL contains only (fragment length) for each enzyme type.
> - for ACS: http://www.aroma-project.org/node/100 (importing from Affymetrix
> probe-tab file) and using the affymetrix files: GenomeWideSNP_6.CN_probe_tab
> and GenomeWideSNP_6.probe_tab.
ACS contains only probe sequences and strandiness. This file will
never have to be updated, because does not depend on the genome only
on the chip probes, which never changes.
> - CDF file: i downloaded the library file genomewidesnp6_libraryfile from
> affymetrix website and extracted the GenomeWideSNP_6.cdf file
A CDF contains (unit name, probesets) and a little bit more. This
rarely gets updated, even if the genome is reannotated; at most there
are only minor updates.
> For segmentation I used both CBS and GLAD, but the issue remain.
Both, and any other segmentation method, will pull the genome position
for loci from the UGP file.
> Could someone help me ?
Hope the above helped.
Finally, having probe positions shifted +/-13 nucleotides should make
no difference to your final conclusions. The distance between loci is
100 times greater, which means that is the best precision you can wish
for from the segmentation, and this without discussing the
segmentation error/uncertainty due to signal noise.
Henrik
>
> Thank you very much,
>
> Cristian
>
>
> --
> 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.
>
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version of the package, 2) to report the output of sessionInfo() and
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