Mercurial > repos > yhoogstrate > edger_with_design_matrix
changeset 40:d9c9caf4e182 draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Thu, 22 May 2014 10:27:38 -0400 |
| parents | 1b8ecb48f6e7 |
| children | 0bbf79213970 |
| files | edgeR_Differential_Gene_Expression.xml |
| diffstat | 1 files changed, 12 insertions(+), 12 deletions(-) [+] |
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--- a/edgeR_Differential_Gene_Expression.xml Thu May 22 10:16:58 2014 -0400 +++ b/edgeR_Differential_Gene_Expression.xml Thu May 22 10:27:38 2014 -0400 @@ -277,15 +277,15 @@ ## change e into epsilon somehow dev.off() } - - if(output_heatmap_plot != "/dev/null") { - pdf(output_heatmap_plot) - etable2 <- topTags(lrt, n=100)\$table - order <- rownames(etable2) - cpm_sub <- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),] - heatmap(t(cpm_sub)) - dev.off() - } + } + + if(output_heatmap_plot != "/dev/null") { + pdf(output_heatmap_plot) + etable2 <- topTags(lrt, n=100)\$table + order <- rownames(etable2) + cpm_sub <- cpm(dge,normalized.lib.sizes=TRUE,log=TRUE)[as.numeric(order),] + heatmap(t(cpm_sub)) + dev.off() } ##output_hierarchical_clustering_plot = args[13] @@ -332,11 +332,11 @@ </data> <data format="RData" name="output_RData_obj" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R data object"> - <filter>("make_output_R" in outputs)</filter> + <filter>("make_output_RData_obj" in outputs)</filter> </data> - <data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output" > - <filter>("make_output_RData_obj" in outputs)</filter> + <data format="txt" name="output_R" label="edgeR DGE on ${design_matrix.hid}: ${design_matrix.name} - R output (debug)" > + <filter>("make_output_R" in outputs)</filter> </data> </outputs>