[BioC] Loading quantiles normalized root data in XPS

[Paul Geeleher]

Hi,

I've used xps to quantiles normalize (at probe level) some Affy Exon
Array data. I now have a "root" file called "exon_quantiles.root", but
if I try to load it the same was I'd load my raw data (using the
scheme file I created for Affy exon arrays) I get the error below? I
can load my raw data just fine though. Any ideas? Do I perhaps need a
different "root scheme" file for this normalized data? Unfortunately,
I haven't been able to find an answer.

> scheme.huex10stv2 <- root.scheme("huex10stv2.root")
> data_qn <- root.data(scheme.huex10stv2, "exon_quantiles.root")
Error in if (chipname != treetitle) { : argument is of length zero

Hope someone can help,

Paul.



> sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-redhat-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base



-- 
Paul Geeleher (PhD Student)
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com