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Posts by prat
... Why are false neg rates usually not seen/used for RNASeq analysis? My guess is that the TP is not known... Is it possible to still calculate/estimate the FNR in DESeq2/edgeR? ...
... How are multiple conditions/comparisons done in v1.16 using lfcShrink? Using the example from the package, eg. cnts <- matrix(rnbinom(n=1500, mu=100, size=1/0.5), ncol=15) cond <- factor(rep(1:3, each=5)) # object construction dds <- DESeqDataSetFromMatrix(cnts, DataFrame(cond), ~ cond) ...
... My design matrix is below for an RNASeq experiment and somewhat similar to Section 3.4.2 Blocking in the manual I'm trying to follow, sample condition mouse ctrl_minus_1 ctrl_minus 1 ctrl_plus_1 ctrl_plus 1 ko_minus_1 ko_minus 2 ko_plus_1 ko_plus 2 ctrl_minus_2 ctrl ...
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