[BioC] arrayQualityMetrics package - bugs and errors

[Martin Morgan]

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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