[BioC] imageplot error message

[Ina Hoeschele]

Hi Mark, Mike et al.,
  when doing imageplots for the beadlevel data, I get the following error message (same thing happens when I specify squareSize). Any suggestion why this happens? Thanks ...

imageplot(BLData,array=1,low="lightgreen",high="darkgreen",horizontal=FALSE)   

Error in res[rowIdx, ] <- resList[[i]][j, ] : 
  number of items to replace is not a multiple of replacement length

> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] geneplotter_1.28.0   lattice_0.19-13      annotate_1.28.0     
 [4] AnnotationDbi_1.12.0 RColorBrewer_1.0-2   gplots_2.8.0        
 [7] caTools_1.11         bitops_1.0-4.1       gdata_2.8.1         
[10] gtools_2.6.2         beadarray_2.0.4      Biobase_2.10.0      

loaded via a namespace (and not attached):
[1] BeadDataPackR_1.2.1 DBI_0.2-5           limma_3.6.9        
[4] RSQLite_0.9-4       tools_2.12.1        xtable_1.5-6       

----- Original Message -----
From: "Ina Hoeschele" <inah at vbi.vt.edu>
To: "Mark Dunning" <mark.dunning at gmail.com>
Cc: bioconductor at stat.math.ethz.ch
Sent: Friday, February 25, 2011 5:03:51 PM
Subject: Re: expressionQCPipeline

Hi Mark,
  thanks much for all your emails. Sorry for bothering you with this really silly problem once more.

<<
Regarding your expressionQCPipeline problem; it should be trying to
write plots to a directory called "QC.Dir[iChip]". If you run

dir("QC.Dir[iChip]")

what does it return?
>>

it created a directory within the current working directory with the name QC.Dir[iChip].
So then I deleted this directory, closed R, and then rerun this code:

library(beadarray)
library(gplots)
library(RColorBrewer)
library(geneplotter)

nChips <- 8
Chip.Dir <- c("C:/5655508006","C:/5655508014","C:/5655508045","C:/5655508059","C:/5655735016","C:/5655735017","C:/5655735018","C:/5655735079")

iChip <- 1

setwd(Chip.Dir[iChip])
BLData = readIllumina(useImages=FALSE, illuminaAnnotation="Humanv4")

expressionQCPipeline(BLData,transFun=logGreenChannelTransform,qcDir="QC",plotType=".jpeg",horizontal=TRUE,controlProfile=NULL,
	overWrite=FALSE,nSegments=9,outlierFun=illuminaOutlierMethod,tagsToDetect=list(housekeeping="housekeeping",Biotin="phage_lambda_genome",
	Hybridisation="phage_lambda_genome:high"),zlim=c(5,7),positiveControlTags=c("housekeeping","phage_lambda_genome"),
	hybridisationTags=c("phage_lambda_genome:low","phage_lambda_genome:med","phage_lambda_genome:high"),negativeTag="permuted_negative",
	boxplotFun=logGreenChannelTransform,imageplotFun=logGreenChannelTransform)


Then it still gives me the message that the plots already exist! It created a sub-directory QC within the C:/5655508006 directory, as it is supposed to. 
The box-plots look fine, and there are several excel files containing information (detectionMetrics, outlierMetrics etc.). But the plots contained in hyb, 
imageplot, outliers and poscont are all empty.