[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)
locale:
[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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