[BioC] expressionQCPipeline

[Ina Hoeschele]

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.