Processing Illumina HumanHT-12 V4.0 data without detection p-values

Processing Illumina HumanHT-12 V4.0 data without detection p-values

1

Hello, I want to pre-process GSE17048 dataset from GEO. I followed the steps provided by Kevin in this post but I realized that neqc from limma requires the detection p-values of each probe for normalizing the data. I wanted to know if there was a way to background correct and normalize the data without using the pvalues.

Thank you.


Illumina


HumanHT-12v4


pre-processing


limma

• 109 views

The group that deposited the data hasn’t done you any favors. Without either the control probes or the detection p-values, it is not possible to use limma’s neqc method. But you can use the normexp background correction method instead:

> library(limma)
> y.raw <- read.delim("GSE17048_non-normalized_data.txt.gz",row.names=1)
> y.bgcorrected <- backgroundCorrect(y.raw, method="normexp")
> y.norm <- normalizeBetweenArrays(log2(y.bgcorrected), method="quantile")


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