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#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)
 
#Pause here to consider a mistake I made yesterday

 
 
down_gene_data <- subset(upsig_gene_data, (log2_fold_change < -1))
nrow(up_gene_data)