Hi

I am trying to do a meta analysis of a number of array studies from illumina arrays ht-v3 and I normally just use limma to remove the background with their neqc function, but data on GEO does not have control probe files for me to read in. There just is one raw non normalised file for everything. So do I just miss out background correction and quantile normalise?

Thanks,

Chris

The neqc() function can work with detection p-values instead of control probes. For example, if x is an EListRaw object with no control probes, but x$other$Detection contains detection p-values, then

y <- neqc(x)

will give the same result as if you have provided the negative control probes.

Usually GEO will provide detection p-values even if it doesn't provide control probes.

See Question about neqc and GEO illumina files for a code example.