lumi **

Lumi is an ongoing project for Illumina microarray data analysis, including the design of a software package in R/Bioconductor and the discussion of microarray experiment design.

** an open source project at the Bioinformatics Core of the Robert H. Lurie Comprehensive Cancer Center, Northwestern University.


Data format for the Lumi Package

How to generate a microarray output file to be analyzed by the lumi package in bioconductor? From the Illumina BeadStudio software, select "> File> Export to GeneSpring > Group Probe Profile". A file called "Group Probe Profile.txt" will be generated. That's it!

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Blogger Ross Lazarus said...

Thanks for publishing this, and it may work where you have set up groups, but the 'group probe profile' choice will only ever export a single 'Default Group' sample export for us which appears to be a grand mean.

We had to use the sample probe profile report to get all the values like bead stdev and so on are exported for each sample.

5:02 PM  

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