Hi,

I am using lumi to normalize Illumina raw Data, but when I run the script, I retrive the following message.

library("lumi")

file = 'BCCSED.txt'
x.lumi = lumiR.batch(file, lib.mapping = 'lumiHumanIDMapping')

Inputting the data ...

Adding nuID to the data ...

No Quality Control assessment of the object because it is not a "LumiBatch" object.

PS: the input raw data file has "ProbeID" and "AVG_Signal" columns of various samples. Is this information enough for normalization or the file should also have "TargetID", "BEAD_STDEV", "AVG_NBEADS", "Detection".

Looking forward to your response. Thank you in Advance.

No, if you only have the AVE_Signal column then you can't do any Illumina-specific normalization or background correction. You will just have to background correct and normalize as you would generic microarray data.

The lumi package can still add nuIDs, which some people like to use for attaching annotation.