[BioC] Problem with BGandNorm() from the Agi4x44PreProcess package

[Wolfgang Huber]

Hi Dick

I have no specific understanding of this, but I would suggest trying 
with a current release of R (2.13) and Bioconductor (2.8), e.g. 
Agi4x44PreProcess 1.12.0

	Best wishes
	Wolfgang


Il May/6/11 8:20 PM, Dick Beyer ha scritto:
> Hello,
>
> I've run into a problem that looks like the function BGandNorm() is broken because it relies on vsn as a method called by normalizeBetweenArrays, but that method has been replaced by a function normalizeVSN().
>
> Here is some output that shows the problem:
>
>> dd<- read.AgilentFE(targets, makePLOT=FALSE)
> Read US23502338_252643710125_S01_GE1_107_Sep09_1_4.txt
> Read US23502338_252643710125_S01_GE1_107_Sep09_1_3.txt
> Read US23502338_252643710125_S01_GE1_107_Sep09_1_2.txt
> Read US23502338_252643710125_S01_GE1_107_Sep09_1_1.txt
>
>
>    RGList:
>          dd$R:   'gProcessedSignal'
>          dd$G:   'gMeanSignal'
>          dd$Rb:  'gBGMedianSignal'
>          dd$Gb:  'gBGUsed'
>
>
>> ddNORM = BGandNorm(dd, BGmethod = "normexp", NORMmethod = "vsn",
> +                    foreground = "MeanSignal", background = "BGMedianSignal",
> +                    offset = 0, makePLOTpre = FALSE, makePLOTpost = FALSE)
> BACKGROUND CORRECTION AND NORMALIZATION
>
>          foreground: MeanSignal
>          background: BGMedianSignal
> Array 1 corrected
> Array 2 corrected
> Array 3 corrected
> Array 4 corrected
> Error in normalizeBetweenArrays(ddBG$G, method = NORMmethod) :
>    vsn method no longer supported. Please use normalizeVSN instead.
>
>
>> ddNORM = BGandNorm(dd, BGmethod = "normexp", NORMmethod = "normalizeVSN",
> +                    foreground = "MeanSignal", background = "BGMedianSignal",
> +                    offset = 0, makePLOTpre = FALSE, makePLOTpost = FALSE)
> BACKGROUND CORRECTION AND NORMALIZATION
>
> Error in BGandNorm(dd, BGmethod = "normexp", NORMmethod = "normalizeVSN",  :
>    NORMmethod should be one of 'none', 'quantile','vsn'
>
>
>> sessionInfo()
> R version 2.12.2 (2011-02-25)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=C
>   [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Agi4x44PreProcess_1.10.0 genefilter_1.32.0        annotate_1.28.1          AnnotationDbi_1.12.0     limma_3.6.9
> [6] Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] DBI_0.2-5       RSQLite_0.9-4   splines_2.12.2  survival_2.36-5 xtable_1.5-6
>
> Cheers,
> Dick
> *******************************************************************************
> Richard P. Beyer, Ph.D.	University of Washington
> Tel.:(206) 616 7378	Env.&  Occ. Health Sci. , Box 354695
> Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
> 			Seattle, WA 98105-6099
> http://depts.washington.edu/ceeh/members_fc_bioinfo.html
> http://staff.washington.edu/~dbeyer
>
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-- 


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