$VAR1 = {
          'cold' => [
                      'cold_01',
                      'cold_02',
                      'cold_03',
                      'cold_04',
                      'cold_05',
                      'cold_06',
                      'cold_07',
                      'cold_08',
                      'cold_09'
                    ],
          'ambient' => [
                         'ambient_01',
                         'ambient_02',
                         'ambient_03',
                         'ambient_04',
                         'ambient_05',
                         'ambient_06',
                         'ambient_07',
                         'ambient_08',
                         'ambient_09'
                       ]
        };
CMD: R --no-save --no-restore --no-site-file --no-init-file -q < salmon.gene.counts.matrix.ambient_vs_cold.ambient.vs.cold.EdgeR.Rscript
> if (! require(edgeR)) {
+    source("https://bioconductor.org/biocLite.R")
+    biocLite("edgeR")
+    library(edgeR)
+ }
> 
> data = read.table("/gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/salmon.gene.counts.matrix", header=T, row.names=1, com='')
> col_ordering = c(2,3,5,9,10,11,15,16,17,1,4,6,7,8,12,13,14,18)
> rnaseqMatrix = data[,col_ordering]
> rnaseqMatrix = round(rnaseqMatrix)
> rnaseqMatrix = rnaseqMatrix[rowSums(cpm(rnaseqMatrix) > 1) >= 2,]
> conditions = factor(c(rep("ambient", 9), rep("cold", 9)))
> 
> exp_study = DGEList(counts=rnaseqMatrix, group=conditions)
> exp_study = calcNormFactors(exp_study)
> exp_study = estimateDisp(exp_study)
Design matrix not provided. Switch to the classic mode.
> et = exactTest(exp_study, pair=c("ambient", "cold"))
> tTags = topTags(et,n=NULL)
> result_table = tTags$table
> result_table = data.frame(sampleA="ambient", sampleB="cold", result_table)
> result_table$logFC = -1 * result_table$logFC
> write.table(result_table, file='salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results', sep='	', quote=F, row.names=T)
> write.table(rnaseqMatrix, file='salmon.gene.counts.matrix.ambient_vs_cold.edgeR.count_matrix', sep='	', quote=F, row.names=T)
> source("/gscratch/srlab/programs/trinityrnaseq-v2.9.0/Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R")
> pdf("salmon.gene.counts.matrix.ambient_vs_cold.edgeR.DE_results.MA_n_Volcano.pdf")
> plot_MA_and_Volcano(rownames(result_table), result_table$logCPM, result_table$logFC, result_table$FDR)
> dev.off()
null device 
          1 
>