YASMA - Yet Another Statistical Microarray Analysis: A Quick Tutorial (for version 0.19) (2002)

by Lorenz Wernisch.

YASMA is an add-on library for the R statistical package and can be used to analyse simple replicated experiments. We are interested in bacterial genes over- or under-expressed in mutants as compared to the wild type. For this purpose, multiple mRNA samples from di®erent cell cultures are hybridized on several arrays. As long as the same number of arrays is used for each sample a straightforward ANOVA analysis can be applied to the series of experiments (a balanced factorial design). From the standard error of the ANOVA anova analysis (or a bootstrap estimate of it) p-values for di®erential expression can be derived. Even if you are not yet familiar with R this tutorial will give you a ¯rst idea of how R and YASMA works. Making full use of features of YASMA and R requires some knowledge of R. I recommend going through the R tutorial on the R online help page, especially the introductory chapters and the chapters on arrays, reading data, loops, writing functions, and on statistical models (YASMA supports model formulas). [via]

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YASMA - Yet Another Statistical Microarray Analysis: A Quick Tutorial (for version 0.19) (2002)

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