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.



We noticed that the column names of BeadStudio output changed when upgrading from v2 to v3.

We emailed the technical support of Illumina, and got the following answer:

In BeadStudio v3 we renamed the column BEAD_STDEV (in v2) to BEAD_STDERR
(in v3) to more accurately reflect the statistic. This change was made
in BeadStudio 2.3.47 update last year. The values reported are the

By the way, we also got an explanation of the p-val v.s. detection-score:

Both BeadStudio versions 2 and 3 report Detection-pval where a number
close to 0 indicates a high confidence of detection above background.
You may remember that BeadStudio v1.5 reported Detection Score which is
1-(p value). The Detection Score was the inverse (near 1 meant high


Available in differential analyses the concordance column reports on the concordance
between Diff Score between multiple probes for the same transcript (as
in DASL projects). Typically there are 3 or more probes per gene in
DASL assay pools and concordance is another way to gauge the reliability
of your Diff Score measurement.

Array standard deviation (ARRAY_STDEV) is the calculated standard
deviation between beadtype data for a given probe from the arrays in a
group when multiple arrays are assigned to the same group (array to
array variation). Bead standard error (BEAD_STERR) refers to the
calculated standard error (standard deviation in beadtype signal /
number of beads per beadtype) in the beadtype average signal within a
group (bead to bead variation).