[BioC] arrayQualityMetrics package - bugs and errors

[Vladimir Krasikov]

Thanks Martin

It fixes the installation problem

Vladimir

On Wed, 15 Feb 2012 15:40:09 +0100, Martin Morgan <mtmorgan at fhcrc.org>  
wrote:

> On 02/15/2012 04:44 AM, Vladimir Krasikov wrote:
>> Dear list
>>
>> While trying to analyze my data with arrayQualityMetrics (thanks to
>> Axel Klenk for the advise to use it) first on PC and now on MAC.
>> I realize that it is can't run at all on MAC, while on PC it does work,
>> although not as described (or at least not all features described in the
>> vignette are functional)
>>
>> 1. MAC story first:
>> It cann't be loaded without affyPLM (so I guess arrayQualityMetrics
>> DEPENDS on affyPLM,
>> and probably on all other packages which are listed in imports field)
>
> Install packages using
>
>    source("http://bioconductor.org/biocLite.R")
>    biocLite("arrayQualityMetrics")
>
> this will install the package and all its dependencies (including  
> imports). See also the instructions at
>
>    http://bioconductor.org/install
>
> You might be prompted to update additional packages, which you should do.
>
>>> library(arrayQualityMetrics)
>> Creating a generic function for ‘boxplot’ from package ‘graphics’ in
>> package ‘affyPLM’
>> Creating a generic function for ‘hist’ from package ‘graphics’ in
>> package ‘affyPLM’
>> Error in as.environment(pos) :
>> no item called "newtable" on the search list
>
> This is an unusual error and it would be good to know if it is repeated  
> when your packages have been installed and updated correctly. If it does  
> still occur, I think you can perhaps provide a bit of debugging  
> information if you say
>
>    trace(loadNamespace, quote(print(package)))
>    library(arrayQualityMetrics)
>
> Martin
>
>> In addition: Warning message:
>> In objects(newtable, all.names = TRUE) :
>> ‘newtable’ converted to character string
>> Error: package/namespace load failed for ‘arrayQualityMetrics’
>>
>> MAC sessionInfo:
>>> sessionInfo()
>> R version 2.14.1 (2011-12-22)
>> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>>
>> locale:
>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] vsn_3.22.0 Biobase_2.14.0 limma_3.10.2
>>
>> loaded via a namespace (and not attached):
>> [1] affy_1.32.1 affyio_1.22.0 BiocInstaller_1.2.1 grid_2.14.1
>> lattice_0.20-0
>> [6] preprocessCore_1.16.0 tools_2.14.1 zlibbioc_1.0.0
>>>
>>
>> #################
>> 2. PC sorry next:
>>
>> Installation also required to install all packages one-by-one from the
>> "imports"
>>
>> I think it doesn't work properly with objects generated by limma (or at
>> least in my case):
>>
>> I did generic import of 61x44K Agilent two-colours microarrays:
>>> RG <- read.maimages(files....)
>> and background correction
>>> RG.b <- backgroundCorrect(RG.raw, method="minimum", offset=50)
>>> arrayQualityMetrics(expressionset = RG.b, outdir =
>>> "D:/R2/Out/Report.61.Rq", force = TRUE)
>> produces 18 warnings of this type:
>>> warnings()
>> 18: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
>> Binning grid too coarse for current (small) bandwidth: consider
>> increasing 'gridsize'
>>
>> If to create MA from RG with: >MA <- MA.RG(RG.b)
>>
>> It doesn't work with MAlist objects at all,
>> and it is not able to create phenoData for RGlist also (which is quite a
>> pity)
>> [I can't reproduce it on MAC, as I can't start the package at all,
>> I will update this error tomorrow from PC]
>>
>> The rest of the report is generated well for the RG object
>>
>> PC sessionInfo:
>>> sessionInfo()
>> R version 2.14.1 (2011-12-22)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.1252
>> [3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C
>> [5] LC_TIME=Dutch_Netherlands.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] arrayQualityMetrics_3.10.0 Biobase_2.14.0 limma_3.10.2
>>
>> Dear authors of arrayQualityMetrics, may you comment?
>>
>> With kind regards
>> Vladimir
>>
>>
>>
>>
>>
>
>


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