Hi,

Thanks for reporting this bug.  When using the .locs file each array segment
is processes seperately to produce the imageplot.  This bug manifests itself
if the width of the segments in pixels differs modulo the squareSize
argument.  I thought I had patched this, but clearly not.

My advice would be to increase the squareSize argument (the default for
BeadChips is 50 pixels, so something larger than that) and try running it
again.

Alternatively set the useLocs argument to FALSE and beadarray will infer the
network of neighbouring beads itself.  This issue won't be a problem then,
but it has the downside of being both slower and not showing the seperation
between individual array segments.  Nonetheless it will still give a good
indication of the intensities across the array.

I hope that is of some help

------------------------------------------------
Mike Smith
PhD Student
Computational Biology Group
Cambridge University


On Sat, Nov 6, 2010 at 1:52 AM, Ying W <daiyingw@gmail.com> wrote:

> Hi Dr Mike Smith,
> I have a problem with the imageplot() command in the latest beadarray but
> it only occurs when I have a .locs file in the same directory.
> > library(beadarray)
> > BLData = readIllumina(dir = "4690176049", useImages = FALSE,
> illuminaAnnotation = "Humanv3", metricsFile = "Metrics.txt")
> ....
> > imageplot(BLData, array = 1, low = "lightgreen", high = "darkgreen",
> squareSize = 25)
> Error in res[rowIdx, ] <- resList[[i]][j, ] :
>   number of items to replace is not a multiple of replacement length
> > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i486-pc-linux-gnu (32-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] 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] beadarray_2.0.2 Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] BeadDataPackR_1.2.0 limma_3.6.6         tools_2.12.0
>
> I was trying to troubleshoot it for a bit and at the line with "rowIdx <-
> 1"
> > dim(res)
> [1] 359  41
> some other information:
> length(resList) == 9
> nrow(resList[[i]]) == 39
> When I looked through resList[[i]][j, ] and brings up a list of numbers of
> length 40 or 41 (with NA or NaN in 41st slot) so I'm guessing this could be
> an issue w/stripping NA/NaNs out (not quite sure where tho).
>
> I hope this goes to the correct Mike Smith.
>
> Best,
> Ying Wu
>

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