Illumina ID Mapping library
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@kritikamish99-9648
Last seen 4.2 years ago
India

I am running lumi and i am getting this message : - Please provide Illumina ID Mapping library!

> file <- 'probe_profile.txt'
> x.lumi <-lumiR.batch(x)
Inputting the data ...

Adding nuID to the data ...
Please provide Illumina ID Mapping library!
Perform Quality Control assessment of the LumiBatch object ...
 from where i will get illumia ID mapping library

thank you

lumi illumina beadarray microarray • 2.0k views
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Mike Smith ★ 5.7k
@mike-smith
Last seen 18 hours ago
EMBL Heidelberg / de.NBI

You provide this in the argument lib.mapping passed to lumiR.batch().  If you're using human arrays you probably want something like:

lumiR.batch(x, lib.mapping = 'lumiHumanIDMapping')
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@kritikamish99-9648
Last seen 4.2 years ago
India
Is it compulsory to provide this argument .? Or it just optional .
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It is optional.  If you don't provide a mapping lumi will just use the standard Illumina Probe IDs, rather than their own.  There is some discussion about why you might want to use there in the package vignette here:

http://bioconductor.org/packages/release/bioc/vignettes/lumi/inst/doc/IlluminaAnnotation.pdf

If you want to find out more about the arguments passed to a function you can access the help file by typing ? and the function name e.g.

?lumiR.batch
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ohh okk

thanks mike

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