[BioC] arrayQualityMetrics package - bugs and errors
Vladimir Krasikov
v.v.krasikov at gmail.com
Thu Feb 16 13:52:23 CET 2012
Dear Wolfgang
Thanks a lot for your advises.
Bellow I provide error messages for my case
On Wed, 15 Feb 2012 19:42:27 +0100, Wolfgang Huber <whuber at embl.de> wrote:
> 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?
Thanks, log-transformation indeed resolves warnings.
And also this step brought some meaning to the Report.
> You say "it doesn't work with MAlist objects at all". Can you please
> provide the exact error message and a reproducible example?
arrayQualityMetrics(expressionset = MA, outdir = "D:/R2/Out/Report", force
= TRUE, do.logtransform=TRUE)
The directory 'D:/R2/Out/Report' has been created.
Error in as(expressionset, "NChannelSet") :
no method or default for coercing "MAList" to "NChannelSet"
Error in prepdata(expressionset, intgroup = intgroup, do.logtransform =
do.logtransform) :
Argument 'expressionset' is of class 'MAList', and its automatic
conversion into 'NChannelSet' failed. Please try to convert it manually.
> 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.
I guess pData method is not defined for the RGList (and the MAList) object
and arrayQualityMetrics first tries to set phenoData for the RGList and
then to convert it to the NChannelSet
pData(RG)$Cy3 <- targets$Cy3
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "pData", for signature
"RGList"
> 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.
And above solution works perfect and add some colors to otherwise nice
report.
Thanks a lot
Vladimir
and as recommended 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
LC_MONETARY=Dutch_Netherlands.1252
[4] LC_NUMERIC=C LC_TIME=Dutch_Netherlands.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] convert_1.30.0 marray_1.32.0
arrayQualityMetrics_3.10.0 Biobase_2.14.0
[5] limma_3.10.2 BiocInstaller_1.2.1
loaded via a namespace (and not attached):
[1] affy_1.32.1 affyio_1.22.0 affyPLM_1.30.0
annotate_1.32.1
[5] AnnotationDbi_1.16.16 beadarray_2.4.1 Biostrings_2.22.0
Cairo_1.5-1
[9] cluster_1.14.2 DBI_0.2-5 genefilter_1.36.0
grid_2.14.1
[13] Hmisc_3.9-2 hwriter_1.3 IRanges_1.12.6
KernSmooth_2.23-7
[17] lattice_0.20-0 latticeExtra_0.6-19 preprocessCore_1.16.0
RColorBrewer_1.0-5
[21] RSQLite_0.11.1 setRNG_2009.11-1 splines_2.14.1
survival_2.36-12
[25] SVGAnnotation_0.9-0 tools_2.14.1 vsn_3.22.0
XML_3.9-4.1
[29] xtable_1.7-0 zlibbioc_1.0.0
>
> 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
>>
>>
>>
>>
>>
>
>
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