[BioC] illumina: how to retrieve annotation information out of tif-files?
Matt.Ritchie at cancer.org.uk
Fri Mar 7 12:29:54 CET 2008
To my knowledge, there is no way of extracting the chip type information
from the text and tif files output by BeadScan. It would be useful though.
This information may be available in some of the other files output by
BeadScan (.idat, .locs, etc) containing the raw data. However, these files
are in proprietary format which only BeadStudio knows how read at present.
Try emailing Illumina's technical support (techsupport at illumina.com) if you
want to find out more about the various files.
> Dear list,
> I recently started dealing with illumina-data, therefor I am currently
> working through the example datasets provided by the 'beadarray' vignette.
> Here, information on the annotation of the chip used is stored in
> 'Human_WG-6.csv' (considering the 'BeadLevelExample' data).
> When dealing with Affymetrix *.CEL.[gz] files, it is possible to
> directly extract chip information via 'gzip -dc foo.CEL.gz | grep
> which yields stl
> 'DatHeader=[38..46177] . . . .. HG_U95Av2.1sq
> I am now wondering if such kind of information can also be extracted out
> of illumina tif-files (if for whatever reason the annotation file is nor
> Thanks for any help.
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