[Bioc-devel] normalize.oligoBatch.quantiles

[Tim Strom]

I notized normalize.oligoBatch.quantiles in oligo.0.0.8

I tried to use it to normalize 9 50K-Hind chips.
The function completed without error message. However
I get back the original data, but not normalized data.
(Please see attached protocol).

If someone is interested, I can provide the environment
and the example files.

Tim

  files<-list.celfiles()
 > mydata<-read.celfiles(files)
Incompatible phenoData object. Created a new one.
 > normq.mydata<-normalize.oligoBatch.quantiles(mydata,"separate")
gn<-geneNames(mydata)
 > gn<-geneNames(mydata)
 > pm(mydata,gn[1])
......
                  27739_Hind.CEL
SNP_A-1641748.1            1282
SNP_A-1641748.2            1722
SNP_A-1641748.3            2151
SNP_A-1641748.4             998
SNP_A-1641748.5             975
SNP_A-1641748.6            1318
SNP_A-1641748.7             989
SNP_A-1641748.8            1375
SNP_A-1641748.9             639
SNP_A-1641748.10            784
SNP_A-1641748.11           2231
SNP_A-1641748.12           1890
SNP_A-1641748.13           2270
SNP_A-1641748.14           2285
SNP_A-1641748.15           1434
SNP_A-1641748.16           2689
SNP_A-1641748.17           1643
SNP_A-1641748.18           1539
SNP_A-1641748.19           1804
SNP_A-1641748.20            726
 > pm(normq.mydata,gn[1])
.......
                  27739_Hind.CEL
SNP_A-1641748.1            1282
SNP_A-1641748.2            1722
SNP_A-1641748.3            2151
SNP_A-1641748.4             998
SNP_A-1641748.5             975
SNP_A-1641748.6            1318
SNP_A-1641748.7             989
SNP_A-1641748.8            1375
SNP_A-1641748.9             639
SNP_A-1641748.10            784
SNP_A-1641748.11           2231
SNP_A-1641748.12           1890
SNP_A-1641748.13           2270
SNP_A-1641748.14           2285
SNP_A-1641748.15           1434
SNP_A-1641748.16           2689
SNP_A-1641748.17           1643
SNP_A-1641748.18           1539
SNP_A-1641748.19           1804
SNP_A-1641748.20            726

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Tim M. Strom				Tel: +49 89 3187 3296
Institut fuer Humangenetik		Fax: +49 89 3187 3297
Ingolstaedter Landstr. 1
85764 Neuherberg
Germany

WWW: http://ihg.gsf.de