Normalisation of protein micro array data using VSN
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keniajin • 0
@keniajin-21042
Last seen 7 weeks ago
Kenya

I am handling protein microarray where the lab slides were scanned and data generated using a Genepix 4,000 B scanner coupled to the GenePix Pro & Microarray Acquisition and Analysis Software (Molecular Devices). Once the data is extracted, I subtract the background noise and purification-tag intensities (here is the lab project). The data from this type of experiments have a mean-variance dependence. I am using VSN package to handle this issue. I am just wondering how the VSN using the vsn2 function handles the negative intensities and it has an inbuilt log2 as per the explanation on the VSN documentation.

microarray normalization protein • 303 views
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@wolfgang-huber-3550
Last seen 6 weeks ago
EMBL European Molecular Biology Laborat…

Dear Keniajin,

please check the article Variance stabilization applied to microarray data calibration and to the quantification of differential expression DOI: 10.1093/bioinformatics/18.suppl_1.s96

PDF at https://www-huber.embl.de/pub/pdf/huber_ismb2002.pdf

Hope this helps,

Wolfgang

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