[BioC] imageplot error message

[Ina Hoeschele]

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 at gmail.com>
To: "Ina Hoeschele" <inah at vbi.vt.edu>
Cc: "Mark Dunning" <mark.dunning at gmail.com>, bioconductor at 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 at 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 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.
>
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-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University