[BioC] XPS package QC data

[cstrato]

Dear Kirill,

Regarding the error in function 'xpsQAReport()' I have just uploaded to 
Bioconductor version xps_1.20.4 which solves the  problem.

The reason for the error was that in R-3.x function 
tools::buildVignettes() did not work as in earlier versions of R, so I 
had to replace it with:
    Sweave("QAReport.Rnw")
    tools::texi2pdf("QAReport.tex", clean=TRUE)

You should be able to download the new version xps_1.20.4 on Monday.

Best regards,
Christian


On 8/29/13 12:06 AM, cstrato wrote:
> 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
>>>>>>
>>>>>>      _______________________________________________
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>>