Ok thanks.

I thought I'd have a go with other packages as I hit a roadblock with 
methylumi in trying a normalisation.

Thanks again for your help.

Paul

Pan Du wrote:
> Hi Paul
>
> Your data is Illumina Methylation data, not expression data. You need 
> to use "methylumi" package to preprocess the data.
> Actually, Sean Davis also told me this this morning.
>
>
> Pan
>
>
> On 1/18/10 4:43 PM, "Paul Sanfilippo" <prseye@gmail.com> wrote:
>
>     Hi Pan,
>
>     I'm thinking the data is in the wrong format, but am keen to know
>     if there's a way around this (eg remapping column headers)
>
>     > sessionInfo()
>     R version 2.10.1 Patched (2009-12-29 r50852)
>     x86_64-apple-darwin9.8.0
>
>     locale:
>     [1] C/C/en_US/C/C/C
>
>     attached base packages:
>     [1] grid      stats     graphics  grDevices utils     datasets
>     methods
>     [8] base
>
>     other attached packages:
>      [1] lumi_1.12.2          MASS_7.3-4           RSQLite_0.8-1
>      [4] DBI_0.2-5            preprocessCore_1.8.0 mgcv_1.6-1
>      [7] affy_1.24.2          annotate_1.24.1      AnnotationDbi_1.8.1
>     [10] Biobase_2.6.1        ggplot2_0.8.5        digest_0.4.2
>     [13] reshape_0.8.3        plyr_0.1.9           proto_0.3-8
>     [16] JGR_1.7-0            iplots_1.1-3         JavaGD_0.5-2
>     [19] rJava_0.8-1
>
>     loaded via a namespace (and not attached):
>     [1] Matrix_0.999375-33 affyio_1.14.0      lattice_0.17-26
>       nlme_3.1-96
>     [5] tools_2.10.1       xtable_1.5-6
>     >
>
>     This is the data format that I have (I've just included the first
>     subject columns (in yellow))
>
>
>
>     Many thanks.
>
>     Regards,
>
>     Paul
>
>     Pan Du wrote:
>
>
>         Hi Paul
>
>         Please provide more detailed information, or else we cannot
>         help you.
>         For example, please send me the returns of sessionInfo() and
>         also the top
>         twenty lines of your data. I want to know whether it is
>         because you are
>         using outdated packages or data in the wrong format.
>         Thanks!
>
>         Pan
>
>
>         On 1/16/10 5:24 PM, "gilbert feng" <g-feng@northwestern.edu>
>         <mailto:g-feng@northwestern.edu>  wrote:
>
>
>
>
>             From: Paul Sanfilippo <prseye@gmail.com>
>             <mailto:prseye@gmail.com>
>             Date: Sun, 17 Jan 2010 10:16:41 +1100
>             To: <bioconductor@stat.math.ethz.ch>
>             <mailto:bioconductor@stat.math.ethz.ch>
>             Subject: [BioC] lumiR error
>
>             Dear List,
>
>             I'm new to microarray analysis, so go easy.  When I try to
>             import some
>             methylation data using lumiR, I receive the following error:
>
>
>
>
>                 meth<-lumiR("~/desktop/meth_sample.txt")
>
>
>
>             Error in gregexpr("\t", dataLine1) : invalid 'text' argument
>
>             If I specify "sep":
>
>
>
>
>                 meth<-lumiR("~/desktop/meth_sample.txt",sep="\t")
>
>
>
>             Error in strsplit(info[nMetaDataLines + 2], sep)[[1]] :
>                subscript out of bounds
>
>             Does anyone know what might be causing the problem? Can
>             lumiR handle
>             this type of data where headers from BeadStudio are
>             "..._Beta" instead
>             of "..._Signal", etc
>
>             Thank you,
>
>             Paul Sanfilippo
>
>
>
>

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