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

[Dick Beyer]

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BGandNorm() is broken because it relies on vsn as a method called by normalizeBetweenArrays, but that method has been replaced by a function normalizeVSN().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