[BioC] XPS package QC data

cstrato cstrato at aon.at
Fri Aug 16 19:51:31 CEST 2013

Dear Kirill,

Please have a look at chapter 5 of vignette 'xps.pdf', especially 
chapter 5.4 describing class QualTreeSet. See also the corresponding 
help files, e.g. '?plotNUSE'. '?plotRLE', '?plotMAD', '?plotCOI' etc.

Furthermore, please look at function 'xpsQAReport()' which will create a 
quality report 'QAReport.pdf'.

Best regards
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at

On 8/16/13 1:58 PM, b a wrote:
> Dear colleagues,
> I use xps package for my HuGene ST 1.0 array and need some help in quality control. I used arrayQualityMetrics package before new version of R was avaliable which doesn't maintain affy package for ST arrays. ArrayQualityMetrics creates good report with "outliers" assays, which are out of borders (for example, cut-offs for NUSE is 1.1), but I've not seen this in xps.
> Is it possible to receive this data (median and IQR for NUSE or RLE) using xps package?
> Thank you!
> Kirill Prusov
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