[BioC] lumiR error

[Sean Davis]

On Mon, Jan 18, 2010 at 5:55 PM, Paul Sanfilippo <prseye at gmail.com> wrote:
> Ok thanks.
>
> I thought I'd have a go with other packages as I hit a roadblock with
> methylumi in trying a normalisation.

Sorry, Paul.  I have been busy and haven't gotten to looking at your
problem.  I hope to get to that in the next day or so.

Sean


> 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 at 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         using outdated packages or data in the wrong format.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 at northwestern.edu>
>>         <mailto:g-feng at northwestern.edu>  wrote:
>>
>>
>>
>>
>>             From: Paul Sanfilippo <prseye at gmail.com>
>>             <mailto:prseye at gmail.com>
>>             Date: Sun, 17 Jan 2010 10:16:41 +1100
>>             To: <bioconductor at stat.math.ethz.ch>
>>             <mailto:bioconductor at 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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