Reproducing normalized values from raw data in GSE20346
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2.4 years ago
jn_bf • 0

I am trying to process the raw data in GSE20346. The processed data were normalized using a cubic spline algorithm (Illumina BeadStudio V2.0). However, I am trying to reproduce results from a paper published using GSE20346 where they normalized the data using normal-exponential background correction followed by quantile normalization. It does not look like control data were included in the publicly available data. I am using neqc (limma) to perform normexp background correction and quantile normalization, as my understanding is that it can approximate the background when no control data are available.

library(limma)
example = read.ilmn("GSE20346_non-normalized.txt.gz")
y = neqc(example)

The reason I don't believe this yields the correct results is because the paper published using GSE20346 released the normalized data. My results yield values ranging from 6-15, but the paper's processed values range from 0-14. Is there something in the workflow that I am missing, or am I misunderstanding how the neqc function works?

illumina normalization quantile limma neqc • 651 views
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Maybe this isn't exactly what you're looking for but, but GSE20346 has been re-processed and analyzed on our Gemma database:

You can get differential expression analysis from the first link, either by disease state, timepoint or treatment.

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