[BioC] arrayQualityMetrics package - bugs and errors

[Vladimir Krasikov]

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





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