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bulk$contrasts -> bulk$fit.contrasts see ca6bf39 of #19 #21

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Feb 28, 2024
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bulk$contrasts -> bulk$fit.contrasts see ca6bf39 of #19 #21

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bulk$contrasts -> bulk$fit.contrasts see ca6bf39
@micahpf
micahpf committed Feb 28, 2024
commit 4d8e8f107818f529be4a5f73f2704446c863489d
8 changes: 4 additions & 4 deletions R/fitModels.R
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Original file line number Diff line number Diff line change
@@ -57,10 +57,10 @@ fitVoomLm <- function(bulkObj, contr.matrix, block = NULL, sample.weights = TRUE
var.design = var.design,
var.group = var.group,
plot = plotVoom)
bulkObj$contrasts <- limma::contrasts.fit(bulkObj$fit, contrasts = contr.matrix)
bulkObj$contrasts <- limma::eBayes(bulkObj$contrasts, robust=TRUE)
limma::plotSA(bulkObj$contrasts, main="Final model: Mean-variance trend")
bulkObj$de <- limma::decideTests(bulkObj$contrasts, lfc = 0)
bulkObj$fit.contr <- limma::contrasts.fit(bulkObj$fit, contrasts = contr.matrix)
bulkObj$fit.contr <- limma::eBayes(bulkObj$fit.contr, robust=TRUE)
limma::plotSA(bulkObj$fit.contr, main="Final model: Mean-variance trend")
bulkObj$de <- limma::decideTests(bulkObj$fit.contr, lfc = 0)
return(bulkObj)
}

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