Analysis Of Protein Microarray Datasets

Question

[hadasa]

Any one with ideas on available R packages for analysis of protein microarray datasets in particular antigen antibody chips where you have a panel of plasma samples tested against a bunch of antigens? Ideas on how to standardize such datasets and to remove the -ve values? (yes i know of limma :) but am looking for any specialized or dedicated packages or tutorials for analysis of these datasets.

[Sophia]

What is printed on your chips? antibodies (to perform sort of an sandwich ELISA assay) or antigens (type "reverse phase assay", where you want to detect e.g. antibodies from serum samples) printed ?

Answer 1

[Michael]

I just searched bioconductor, there doesn't seem to exist a package dedicated to protein arrays. However, these arrays will be either single- or dual channel arrays, so the standard methods e.g. in limma should apply.

Search found this, have not tried to access, but maybe another option: http://www.pnl.gov/statistics/ProMAT/

And the articles:

• Daly DS, AM White, SM Varnum, KK Anderson, and RC Zangar. "Evaluating concentration estimation errors in ELISA microarray experiments.(Offsite link)" BMC Bioinformatics 2005, 6:17.
• Daly D.S., Anderson, K.K., White, A.M., Gonzalez, R.M., Varnum, S.M., and Zangar, R.C. "Predicting protein concentrations with ELISA microarray assays, monotonic splines and Monte Carlo simulation." Statistical Applications in Genetics and Molecular Biology 2008, 7(1): Article 21

Answer 2

[Rm]

Search within "Bioconductor" modules...

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[hadasa]

Thank you very much!!

Answer 3

[Sophia]

There is QuantPro, a tool for quantitative analysis of 2-antibody-sandwich microarrays.