[BioC] arrayQualityMetrics package - bugs and errors

[Wolfgang Huber]

Dear Vladimir

Thank you for the feedback and the detailed descriptions.

To remove the reason for the warning from KernSmooth::bkde2D (which is 
called by the MA-plots section), please use the argument 
'do.logtransform=TRUE' for the function 'arrayQualityMetrics'. Does that 
resolve your problem?

You say "it doesn't work with MAlist objects at all". Can you please 
provide the exact error message and a reproducible example?

Interoperability of 'RGList' and 'MAList' objects with the rest of 
Bioconductor can be challenging. arrayQualityMetrics uses the 'convert' 
package to convert them into 'NChannelSet', and then works from that. If 
you have problems with the phenoData, please send us a reproducible 
example so we can try to update the conversion code.

As a short term solution to your problem, do the conversion yourself with

library("convert")
x = as(RG, "NChannelSet")

and then set the phenoData of x as you wish.

	best wishes
	Wolfgang

Vladimir Krasikov scripsit 02/15/2012 01:44 PM:
> 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)
>
>> 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
> 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
>
>
>
>
>


-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber