WebSome plots in the cummeRbund package have the option to plot all of the replicates, if there are any. case* and control: you can specify the case and control name in a cufflinks analysis. This makes it much easier to plot 2D graphs (case vs. control) using cummeRbund functions. However, you must have the spellings EXACTLY the same as … WebI also tried the following command in the R software cummeRbund package, but the output answers were as LOCs ID. cuff <- readCufflinks () #Retrive significant gene IDs (XLOC) with a pre-specified alpha diffGeneIDs <- getSig (cuff,level="genes",alpha=0.05) #Use returned identifiers to create a CuffGeneSet object with all relevant info for given ...
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