[BioC] algorithms and explanations

Spencer Spratt spencer.spratt at hertford.oxford.ac.uk
Fri Apr 30 13:00:50 CEST 2004


I'm a biologist, using the bioconductor microarray data analysis software tool to try and gain meaningful biological results from Affymetrix Genechip and Cambridge, uk, Flychip cDNA microarray data.

I would like to understand the numerical values obtained for a comparison analysis using bioconductor, and the equations (algorithms) used to achieve them with a description of what numerical values and how they are used in these equations.

I would appreciate it, if anyone could point me in the direction of the equations used to calculate the Signal value for each probe or probe set, I understand this as being either the RMA or GCRMA equations, and explanations of why either the RMA or GCRMA equation is used.

Also, I'm looking for equations used to calculate Fold change, t.equalvar statistic, raw p-value and the Bonferroni value and explanations of what these mean, especially for t.equalvar and Bonferroni.

Any help would be greatly appreciated

best wishes


Spencer Spratt

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