Question: Illumina ID Mapping library
0
gravatar for kritikamish99
3.7 years ago by
India
kritikamish9910 wrote:

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

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by kritikamish9910
Answer: Illumina ID Mapping library
0
gravatar for Mike Smith
3.7 years ago by
Mike Smith4.0k
EMBL Heidelberg / de.NBI
Mike Smith4.0k wrote:

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 COMMENTlink written 3.7 years ago by Mike Smith4.0k
Answer: Illumina ID Mapping library
0
gravatar for kritikamish99
3.7 years ago by
India
kritikamish9910 wrote:
Is it compulsory to provide this argument .? Or it just optional .
ADD COMMENTlink written 3.7 years ago by kritikamish9910

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 REPLYlink written 3.7 years ago by Mike Smith4.0k

ohh okk

thanks mike

ADD REPLYlink written 3.7 years ago by kritikamish9910
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