[BioC] How do I background correct an Illumina eset without using lumiB

[Gordon K Smyth]

Dear Emma,

Do you have detection p-values for each sample?  If you do, then the 
neqc() function in the limma package can background correction the 
Illumina intensities by automatically reconstructing what the negative 
control values must have been for each array.

See

  http://nar.oxfordjournals.org/content/38/22/e204

for a description of the neqc() method.  Also see the Mammary Stem Cell 
case study in the limma User's Guide for an example of its use.  (The 
published article and the case study assume that control probes are 
available, but the usage with detection p-values is similar.)

Best wishes
Gordon

> Date: Wed, 22 May 2013 03:08:56 -0700 (PDT)
> From: "Emma Bell [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, e.bell12 at imperial.ac.uk
> Cc: lumi Maintainer <dupan.mail at gmail.com>
> Subject: [BioC] How do I background correct an Illumina eset without
> 	using	lumiB?
>
> Hello,
>
> I'm doing some work with publicly available microarray data sets that 
> I've downloaded from GEO. I'm having some trouble using the lumi package 
> to process Illumina BeadArray data.
>
> My understanding is that, normally when using the lumi package you would 
> use lumiR to convert your data to a lumiBatch object, which you could 
> then use lumiB on to background correct. I believe lumiR requires bead 
> standard errors in order to create a lumiBatch object, in their absence 
> it creates an expression set and that lumiB requires the input to be a 
> lumiBatch object. The data sets that I've downloaded only list mean 
> intensity values for each probe and in some cases an associated P-value. 
> Therefore I can't turn my data into lumiBatch object and thus can't 
> background correct with lumiB.
>
> The data sets that I'm trying to use are:
> GSE31978
> GSE30670
> GSE22427
> GSE13674
> GSE20381
>
> I've been using lumiR as follows:
>
>> library(lumi)
>> GSEXXXXX.lumi <- lumiR("GSEXXXXX_Raw_Data.txt",lib.mapping="lumiHumanIDMapping")
>
> I would really appreciate any suggestions on how to background correct 
> these expression sets. Apologies if I've phrased this unhelpfully or 
> left out important information, I'm very new to both R and asking 
> questions to a mailing list like this.
>
> Thanks,
>
> Emma
>
> -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.15.3 (2013-03-01)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252
> [2] LC_CTYPE=English_United Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] lumi_2.10.0        nleqslv_2.0        Biobase_2.18.0     BiocGenerics_0.4.0
> [5] limma_3.14.4
>
> loaded via a namespace (and not attached):
> [1] affy_1.36.1           affyio_1.26.0         annotate_1.36.0
> [4] AnnotationDbi_1.20.7  BiocInstaller_1.8.3   colorspace_1.2-2
> [7] DBI_0.2-5             grid_2.15.3           IRanges_1.16.6
> [10] KernSmooth_2.23-8     lattice_0.20-13       MASS_7.3-23
> [13] Matrix_1.0-11         methylumi_2.4.0       mgcv_1.7-22
> [16] nlme_3.1-108          parallel_2.15.3       preprocessCore_1.20.0
> [19] RSQLite_0.11.2        stats4_2.15.3         XML_3.96-1.1
> [22] xtable_1.7-1          zlibbioc_1.4.0
>

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