Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_DGE.xml @ 14:15fd1a6798e0 draft

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Uploaded
author yhoogstrate
date Thu, 09 Jan 2014 08:29:43 -0500
parents 6e475c849a38
children db9eb4b6f778
comparison
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13:6e475c849a38 14:15fd1a6798e0
104 104
105 empty_samples = apply(read_counts,2,function(x) sum(x) == 0) 105 empty_samples = apply(read_counts,2,function(x) sum(x) == 0)
106 if(sum(empty_samples) > 0) { 106 if(sum(empty_samples) > 0) {
107 write(paste("There are ",sum(empty_samples)," empty samples found:",sep=""),stderr()) 107 write(paste("There are ",sum(empty_samples)," empty samples found:",sep=""),stderr())
108 write(colnames(read_counts)[empty_samples],stderr()) 108 write(colnames(read_counts)[empty_samples],stderr())
109 } 109 } else {
110 else {
111 dge = DGEList(counts=read_counts,genes=rownames(read_counts)) 110 dge = DGEList(counts=read_counts,genes=rownames(read_counts))
112 111
113 design_tmp <- raw_data[3:length(raw_data)] 112 design_tmp <- raw_data[3:length(raw_data)]
114 rownames(design_tmp) <- colnames(dge) 113 rownames(design_tmp) <- colnames(dge)
115 formula = paste(c("~0",colnames(design_tmp)),collapse = " + ") 114 formula = paste(c("~0",colnames(design_tmp)),collapse = " + ")