There is any package for sst-RMA normalization in R?

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6.0 years ago

mgdrnl ▴ 10

Dear all

I am working in a microarray core facility and we realized that the “Signal Space Transformation” (SST-RMA) normalization method, implemented in the Expression Console software, improves the fold-change of the arrays (higher range of fold change) when compared to conventional normalization method RMA (Irizarry et al. 2003).

We would like to implement sst-rma normalization in our R pipeline, but I can't find any R package that performs SST-RMA normalization. Packages like "oligo", "affy" and "aroma.affymetrix" perform RMA but not SST-RMA.

Any help will be most welcome!

affymetrix rma expression console microarray • 2.7k views

ADD COMMENT • link 6.0 years ago by mgdrnl ▴ 10

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There was another recent question where SST-RMA came up, here: RMA with Affymetrix Expression Console vs Oligo package

I am yet to see a R package that implements it - I fear that the algorithm may even be unavailable as it looks like it was developed at Affymetrix / Thermofisher. You may get a more comprehensive answer at Bioconductor support forum where Benilton Carvalho is more active.

ADD REPLY • link 6.0 years ago by Kevin Blighe 88k

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