Processing Illumina HumanHT-12 V4.0 data without detection p-values
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.
• 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")
Traffic: 2000 users visited in the last hour
Read more here: Source link