Hi Pan,

Thank you very much for pointing it out. I asked the lab to include the 
columns and export again. Worked perfectly. I almost finished analysis now.

Thanks!

Xiao-yu

On 6/28/13 1:38 AM, Pan Du wrote:
> Hi Liu X
>
> This is because your data does not include the bead standard error 
> information for the probes (columns are named like "BEAD_STDERR"), 
> which is required for LumiBatch class. If this information is missing, 
> the lumiR will just output an ExpressionSet object. Please check the 
> help of lumiR and the lumi.pdf vignette for more details.
>
>
> Pan
>
>
> On Thu, Jun 27, 2013 at 7:30 PM, Liu X [guest] <guest@bioconductor.org 
> <mailto:guest@bioconductor.org>> wrote:
>
>
>     Hello,
>
>     It is my first time trying to use lumi package to analyze beadchip
>     data by following the instruction in vignettes (dated 2013/4/4).
>     However I run into problems. Trying to use lumiR to read in a
>     beadstudio export file with following commands:
>
>     library(lumi)
>     library(illumi
>     sampfile <- 'path/to/sample_probe_profile.txt'
>     lumi.sample<-lumiR(sampfile, lib.mapping="lumiMouseIDMapping",
>     annotationColumn = c('PROBE_ID', 'SYMBOL', 'ILMN_GENE',
>     'CHROMOSOME', 'DEFINITION', 'SYNONYMS') )
>
>     It runs without error, but class(lumi.sample) tells me that it is
>     an ExpressionSet object not LumiBatch. And of course I cannt apply
>     lumi methods to analyze it.
>
>     What wrong with my steps?
>
>     Thanks!
>


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