[BioC] XPS package QC data

[cstrato]

Dear Kirill,

Regarding the error I have already sent a mail to R-devel and am waiting 
for an answer. I will update xps as soon as I know the reason for this 
error.

Regarding Windows 7 you need a ROOT version compiled with MinGW, as the 
README file mentions. Currently, you should be able to download this 
file from:
https://docs.google.com/file/d/0B0qZ3XBoK1ubVzl5MHBEaWxQdW8/edit

In case the download link does not work, I could send you the ROOT 
binary compiled with MinGW, i.e. root-mingw-O2.7z, however the size is 
35 MB.

Please uninstall the current version of ROOT before installing the 
correct one otherwise there may be problems. Please let me know if you 
can run xps on your Windows machine.

Best regards,
Christian


On 8/28/13 11:34 PM, b a wrote:
> Dear Christian,
>
> I tried to use xps package on Unix and Windows machines. I had your error in tools package on Unix machine, but I couldn't launch xps package on Windows via command "library("xps")"; the error occurred in libCint.dll.
>
> My current machine is Windows 7 and I use newest version of ROOT (5.34)
>
> Regards,
> Kirill
>
>
> 28.08.2013, 23:09, "cstrato" <cstrato at aon.at>:
>> Dear Kirill,
>>
>> To answer your first question: No, the pdf file does not contain more
>> information than shown in the QC stats folder, it is only a conversion
>> of the QAReport.Rnw file.
>>
>> BTW, I have just tried to run function 'xpsQAReport()' and get the
>> following error:
>>
>> Loading required package: tools
>> Error in .get_package_metadata(pkgdir) :
>>     Files 'DESCRIPTION' and 'DESCRIPTION.in' are missing.
>>
>> Is this the error that you get?
>>
>> It seems that function buildVignettes() of the 'tools' package must have
>> changed since this error did not appear in earlier versions of R!!
>> I will ask at the R-devel mailing list what the error might be.
>>
>> BTW, if you want to get also numeric QC values please have a look at
>> function treeInfo() and the examples shown in the help '?treeInfo'.
>>
>> Regarding your second  question:
>> - What is the name of the ROOT binary that you have installed on your
>> current machine? (Is this WinXP?)
>> - What is the name of the ROOT binary that you did install on Windows 7?
>>
>> Best regards,
>> Christian
>>
>> On 8/28/13 10:46 AM, b a wrote:
>>
>>>   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
>>>>>
>>>>>      _______________________________________________
>>>>>      Bioconductor mailing list
>>>>>      Bioconductor at r-project.org
>>>>>      https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>      Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>