Mercurial > repos > yhoogstrate > edger_with_design_matrix

comparison edgeR_Differential_Gene_Expression.xml @ 34:a36a9af266e5 draft

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author yhoogstrate
date Wed, 21 May 2014 05:14:57 -0400
parents 7e45df99a6fc
children fab87cecb3e5
comparison
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33:7e45df99a6fc 34:a36a9af266e5
245 245
246 ## todo EXPORT FPKM 246 ## todo EXPORT FPKM
247 write.table(file=output_raw_counts,dge\$counts,sep="\t",row.names=TRUE,col.names=NA) 247 write.table(file=output_raw_counts,dge\$counts,sep="\t",row.names=TRUE,col.names=NA)
248 248
249 249
250 if(output_MAplot != "/dev/null" or output_PValue_distribution_plot != "/dev/null") { 250 if(output_MAplot != "/dev/null" || output_PValue_distribution_plot != "/dev/null") {
251 etable <- topTags(lrt, n=nrow(dge))\$table 251 etable <- topTags(lrt, n=nrow(dge))\$table
252 etable <- etable[order(etable\$FDR), ] 252 etable <- etable[order(etable\$FDR), ]
253 253
254 if(output_MAplot != "/dev/null") { 254 if(output_MAplot != "/dev/null") {
255 write("Creating MA plot...",stdout()) 255 write("Creating MA plot...",stdout())