Dear Stephen,

You are correct, beadarray is currently only designed to deal with two
swaths.  I haven't previously encountered any data that was split into
three.  I don't know if that's a property of the
chip type or the machine, but I suspect the latter.  Our swath data has all
been generated on the iScan (rather than HiScan) machine.

Thank you very much for posting your data, that's a big help.  It would be
really great if you could include the images too, as I try to use the
images as a verification step in breaking the text file down into the
component parts.  I won't need an entire chip, but the three swaths from
one array section would be great.  I'm afraid I won't get a chance to look
at this until the new year as I'm on holiday from tomorrow, but I shall let
you know when I've made processSwathData() more generalisable over the
number of swaths.

Many thanks

Mike Smith


On Thu, Dec 22, 2011 at 7:55 PM, Stephen Edwards <swandle06@yahoo.com>wrote:

> I'm getting the following error when running processSwathData on files
> from a
> HiScan run on the HumanHT-12 v4.  I'm wondering whether it is due to the
> fact
> that this chip type results in 3 swath files (at least with our instrument)
> instead of one or two as previously discussed
> (
> http://article.gmane.org/gmane.science.biology.informatics.conductor/38045/match=processSwathData
> ).
>  I've posted an example data set (5719680020.tar.gz) on
> ftp://ftp2.cancerresearchuk.org/pub/beadarray/ per the post above.  I
> deleted
> the tif files to reduce the file size, but I get the same error when the
> images
> are included.
>
> processSwathData(twoColour=FALSE,  segmentHeight=1800, segmentWidth=15750)
> 5719680020_A
> Error in cbind(txtFileCoords, locsFileCoords[, c(1,
> 4:ncol(locsFileCoords))]) :
>  number of rows of matrices must match (see arg 2)
> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-unknown-linux-gnu (64-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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=C                 LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] beadarray_2.4.1 ggplot2_0.8.9   proto_0.3-9.2   reshape_0.8.4
> [5] plyr_1.6        Biobase_2.14.0
>
> loaded via a namespace (and not attached):
> [1] AnnotationDbi_1.16.10 BeadDataPackR_1.6.0   DBI_0.2-5
> [4] IRanges_1.12.5        limma_3.10.0          RSQLite_0.11.1
>
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>



-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

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