Content Comparison

#IF YOU HAVE NOT COPIED THIS OVER ALREADY
cds
cd my_rnaseq_course
cp -r /corral-repl/utexas/BioITeam/rnaseq_course_2015/day_3_partB/cuffdiff_results .

IF YOU HAVE ALREADY COPIED IT OVER
cds
cd my_rnaseq_course
cd day_3_partB/cuffdiff_results
 

#We need the cuffdiff results because that is the input to cummeRbund.

#Below command is equivalent to looking at the gene_exp.diff file that we spent a lot of time parsing yesterday
gene_diff_data <- diffData(genes(cuff_data))   
#Do gene_diff_data followed by tab to see all the variables in this data object
 
sig_gene_data  <- subset(gene_diff_data, (significant ==  'yes'))
up_gene_data  <- subset(sig_gene_data, (log2_fold_change > 1))
#How many
nrow(up_gene_data)
  
down_gene_data <- subset(sig_gene_data, (log2_fold_change < -1))
nrow(updown_gene_data)