From 42cfc878ae8cf1c7f03e55e94cf4ca6b731884f6 Mon Sep 17 00:00:00 2001 From: "Lee S. Leavitt" Date: Tue, 13 Feb 2024 16:42:21 -0700 Subject: [PATCH 1/3] bug --- R/samr.morefuns.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/samr.morefuns.R b/R/samr.morefuns.R index 60ffb57..d9136aa 100755 --- a/R/samr.morefuns.R +++ b/R/samr.morefuns.R @@ -577,7 +577,7 @@ samr.compute.siggenes.table = function(samr.obj, del, { res.up = cbind(sig$pup + 1, data$genenames[sig$pup], data$geneid[sig$pup], samr.obj$tt[sig$pup], samr.obj$numer[sig$pup], - samr.obj$sd[sig$pup], samr.obj$stand.contrasts[sig$pup, ], qvalues$qvalue.up) + samr.obj$sd[sig$pup], samr.obj$stand.contrasts[sig$pup, ,drop=F], qvalues$qvalue.up) if (compute.localfdr) { From d10aa884d6f5e09f5182a14cc38cc81e24d4ba6e Mon Sep 17 00:00:00 2001 From: "Lee S. Leavitt" Date: Tue, 13 Feb 2024 20:16:33 -0700 Subject: [PATCH 2/3] fill in na values returned to 0's --- R/samr.R | 3 +++ 1 file changed, 3 insertions(+) diff --git a/R/samr.R b/R/samr.R index 4427c88..b5dd192 100755 --- a/R/samr.R +++ b/R/samr.R @@ -347,6 +347,9 @@ samr <- function(data, resp.type = c("Quantitative", tt <- junk$tt eigengene = junk$eigengene } + + tt[is.na(tt)] <- 0 + #seq data if (resp.type == samr.const.twoclass.unpaired.response & assay.type == "seq") { From aedab595ed991eb3167ce72dc1d0e9c368d42d9d Mon Sep 17 00:00:00 2001 From: "Lee S. Leavitt" Date: Thu, 13 Jun 2024 11:35:41 -0600 Subject: [PATCH 3/3] Revert "fill in na values returned to 0's" This reverts commit d10aa884d6f5e09f5182a14cc38cc81e24d4ba6e. --- R/samr.R | 3 --- 1 file changed, 3 deletions(-) diff --git a/R/samr.R b/R/samr.R index b5dd192..4427c88 100755 --- a/R/samr.R +++ b/R/samr.R @@ -347,9 +347,6 @@ samr <- function(data, resp.type = c("Quantitative", tt <- junk$tt eigengene = junk$eigengene } - - tt[is.na(tt)] <- 0 - #seq data if (resp.type == samr.const.twoclass.unpaired.response & assay.type == "seq") {