[BioC] XPS package QC data

b a haba18 at yandex.ru
Wed Aug 28 10:46:18 CEST 2013

Dear Christian,

Thank you for this answer. I'm trying to use this package for automatic quality control. In arrayQualityMetrics report I can see table with detected outliers (such as here: http://www-huber.embl.de/arrayQualityMetrics/Report_for_nMLL_with_factors/). In the xps package I cannot make my report in pdf because I have some errors, only Rwd file and all images. Does pdf file contain more information than I see into the QC stats folder?

Thank you!

And one more question. I have an error when I launch xps package at Windows 7. The error is "The procedure entry point _ZN18G_FastAllocString6FormatEPKcz could not be located in the dynamic link library libCint.dll"

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: i386-w64-mingw32/i386 (32-bit)

[1] LC_COLLATE=Russian_Russia.1251  LC_CTYPE=Russian_Russia.1251    LC_MONETARY=Russian_Russia.1251 LC_NUMERIC=C                    LC_TIME=Russian_Russia.1251    

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

other attached packages:
[1] BiocInstaller_1.10.3

loaded via a namespace (and not attached):
[1] tools_3.0.1

16.08.2013, 21:51, "cstrato" <cstrato at aon.at>:

>  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
>  Christian
>  _._._._._._._._._._._._._._._._._._
>  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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