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federicomarini / pcaExplorer

pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data
https://federicomarini.github.io/pcaExplorer/
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array-based expression data + pcaExplorer #15

Open guidohooiveld opened 3 years ago

guidohooiveld commented 3 years ago

Hi, This may be a naive question, since I know pcaExplorer has been designed for RNA-seq data, but I am wondering...: would there be an easy way to usepcaExplorer also for array-based expression data? For example, by just providing it both as input for the argument dst and countmatrix? Thanks! G

federicomarini commented 3 years ago

Hi Guido, not a naive question at all! Let's say that most such explorations do require something that recalls a homoscedastic-like dataset. And that'd be the dst object. Well, if you can fit into that some form of normalized/transformed expression values, from microarrays, then it could still work. Maybe make sure to convert the probe ids already to gene symbols (e.g. with the annotation table you can provide?). In principle, some functionality should very much work out of the box, some probably would require some fiddling... HTH, Federico