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 DatHeader'. 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 available). Thanks for any help. Cheers /Christian/

Hi Christian, 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. Best wishes, Matt > 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 > DatHeader'. > 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 > available). > > Thanks for any help. > > Cheers > /Christian/