Question: Analysis Of Protein Microarray Datasets
3
gravatar for hadasa
10.2 years ago by
hadasa1.0k
hadasa1.0k wrote:

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.

R analysis protein microarray • 4.2k views
ADD COMMENTlink modified 5.8 years ago by CanyTon10 • written 10.2 years ago by hadasa1.0k
1

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 ?

ADD REPLYlink written 10.2 years ago by Sophia300
3
gravatar for Michael Dondrup
10.2 years ago by
Bergen, Norway
Michael Dondrup48k wrote:

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
ADD COMMENTlink modified 10.2 years ago • written 10.2 years ago by Michael Dondrup48k
1
gravatar for Rm
10.2 years ago by
Rm8.0k
Danville, PA
Rm8.0k wrote:

Search within "Bioconductor" modules...

These articles might be useful to you...

Pattern Recognition in Pulmonary Tuberculosis Defined by High Content Peptide Microarray Chip Analysis Representing 61 Proteins from M. tuberculosis

Identification of humoral immune responses in protein microarrays using DNA microarray data analysis techniques

ADD COMMENTlink written 10.2 years ago by Rm8.0k

Thank you very much!!

ADD REPLYlink written 10.2 years ago by hadasa1.0k
1
gravatar for Sophia
10.2 years ago by
Sophia300
Barcelona
Sophia300 wrote:

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

ADD COMMENTlink written 10.2 years ago by Sophia300
0
gravatar for CanyTon
5.8 years ago by
CanyTon10
United States
CanyTon10 wrote:

This is going to help you a little bit about your problem!

http://www.biotechniques.com/BiotechniquesJournal/2014/September/RPPanalyzer-Toolbox-An-improved-R-package-for-analysis-of-reverse-phase-protein-array-data/biotechniques-353895.html

ADD COMMENTlink written 5.8 years ago by CanyTon10
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