Question

background correction for illumina array files

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chris86 ▴ 420

@chris86-8408

Last seen 4.4 years ago

UCL, United Kingdom

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

limma microarray • 795 views

ADD COMMENT • link updated 7.5 years ago by Gordon Smyth 50k • written 7.5 years ago by chris86 ▴ 420

score 2 · Accepted Answer · 2016-10-12

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Gordon Smyth 50k

@gordon-smyth

Last seen 3 hours ago

WEHI, Melbourne, Australia

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.

ADD COMMENT • link 7.5 years ago Gordon Smyth 50k

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Thanks again Gordon. I actually have two studies, one illumina ht-v4 and the other ht-v3. Do you recommend I remove the probes not found in both, then rbind and normalise the file as one with NEQC before batch correction? Or should I normalise the data separately then batch correct?

ADD REPLY • link 7.5 years ago chris86 ▴ 420

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Absolutely need to background correct separately. You might be able to normalize together, after consolidating probes, but I'd be nervous about it. Keeping the analyses entirely separate would usually be preferable.

ADD REPLY • link 7.5 years ago Gordon Smyth 50k