Hi Ina,

I've just looked at the code and the call to imageplot() in
expressionQCPipeline() does indeed have useLocs = TRUE, so it's probably the
issue.

I've added the patch we've used in the devel version to release 2.0.6.  If
you update to that, both imageplot() and expressionQCPipeline() should both
work with the locs file.  If it's still causing errors let us know and we'll
add an argument to expressionQCPipeline() allowing the user to toggle the
useLocs argument.

I hope that helps,



On Mon, Mar 7, 2011 at 2:55 AM, Ina Hoeschele <inah@vbi.vt.edu> wrote:

> thank you, Mike, doing the image plots with useLocs = FALSE works and is
> good enough ... Could this also be affecting my attempts to run
> expressionQCPipeline, which includes image plots?
> Ina
>
> ----- Original Message -----
> From: "Mike Smith" <grimbough@gmail.com>
> To: "Ina Hoeschele" <inah@vbi.vt.edu>
> Cc: "Mark Dunning" <mark.dunning@gmail.com>,
> bioconductor@stat.math.ethz.ch
> Sent: Thursday, March 3, 2011 5:28:34 AM
> Subject: Re: [BioC] imageplot error message
>
> Hi Ina,
>
> The simplest solution is to set the argument useLocs = FALSE
>
> By default the image plot function tries to consider each of the segments
> that make up an array section separately, and plot them with a white
> separator.  In order to do this it needs the locs file.  If you choose not
> to use the locs file it will just consider the entire section in one go.
>  This can lead to some artefacts near the breaks between segments, as you
> end up with a small number of beads in a square, but it still gives a
> pretty
> good idea of how the intensities are distributed across the section.
>
> Alternatively, you can upgrade the the developmental version of the
> package,
> where I've added a patch that stops this error from occurring and allows
> the
> use of the locs file (Thanks to Ying Wu for the code).
>
> I hope that helps,
>
> Mike
>
> On Wed, Mar 2, 2011 at 8:51 PM, Ina Hoeschele <inah@vbi.vt.edu> wrote:
>
> > 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@vbi.vt.edu>
> > To: "Mark Dunning" <mark.dunning@gmail.com>
> > Cc: bioconductor@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.
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>
>
>
> --
> Mike Smith
> PhD Student
> Computational Biology Group
> Cambridge University
>



-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

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