illumina microarray analysis using lumi(lumiR) and limma(read.ilmn)

Question

[swordbreadjj]

Hi I'm handling and analyzing illumina microarray datasets.

lumi and illumina r package respectively provide lumiR-lumiExpresso and read.ilmn-neqc functions to preprocess microarray data.

In lumiR function, lib.mapping option is optional, and In read.ilmn function, control probe file is optional but recommended.

If there are NO control probe file, lumiR-lumiExpresso function is more reasonable?

Thanks in advance.

[Kevin Blighe]

Can you elaborate on the format of your data, currently?; and how was it produced? Control probe information would most likely have already been used for the purposes of calculating expression, but, if you don't have the control probe file, then it's not necessary. It would just have been stored in the R object along with all of your other expression and phenotype / annotation data. It depends on what processing has already been performed, though.

[swordbreadjj]

Thank you for comment I'm going to analyze GEO datasets such as GSE35548

[Kevin Blighe]

Usually for the GEO datasets there is sample code that allows you to read in the normalised data. If you click on the 'Analyze with GEO2R' button, and then the 'R script' tab, you'll see code that allows you to do this. Then, you will not have to worry about the control probes.

[swordbreadjj]

Thank you for the kind comments!