[BioC] Loading quantiles normalized root data in XPS

[cstrato]

Dear Paul,

Please have a look at the help ?root.expr.

If I understand you correctly, you did only do quantile normalization?

To see the tree names in your file you should do:
 > getTreeNames("exon_quantiles.root")

You will probably see trees with extension "int", see help ?validTreetype.

To load these trees you need to do:
 > data_qn <- root.expr(scheme.huex10stv2, "exon_quantiles.root", "int")

Please let me know if this did solve your problem.

Best regards
Christian
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On 2/1/12 7:07 PM, Paul Geeleher wrote:
> 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
>
>
>