Question

Illumina ID Mapping library

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kritikamish99 ▴ 10

@kritikamish99-9648

Last seen 6.3 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 • 3.1k views

ADD COMMENT • link 8.8 years ago kritikamish99 ▴ 10

score 0 · Answer 1 · 2016-02-11

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Mike Smith ★ 6.6k

@mike-smith

Last seen 26 minutes ago

EMBL Heidelberg

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')

ADD COMMENT • link 8.8 years ago Mike Smith ★ 6.6k

score 0 · Answer 2 · 2016-02-11

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kritikamish99 ▴ 10

@kritikamish99-9648

Last seen 6.3 years ago

India

Is it compulsory to provide this argument .? Or it just optional .

ADD COMMENT • link 8.8 years ago kritikamish99 ▴ 10

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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

ADD REPLY • link 8.8 years ago Mike Smith ★ 6.6k

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ohh okk

thanks mike

ADD REPLY • link 8.8 years ago kritikamish99 ▴ 10