I'm getting different FPKM values from diffData() and fpkm() on a couple of different isoform IDs
diffData() reports an fpkm of 0 for sample_2 (reported as "value_2")
but fpkm() reports an fpkm of ~0.09 for sample_2
I know that csHeatmap() uses fpkm() to extract values for plotting, but which is the most accurate value?
I thought cuffdiff values (available from diffData()) were supposed to be the most accurate?
Code:
> diffData(getFeatures(cuff,"TCONS_00246566")) isoform_id sample_1 sample_2 status value_1 value_2 log2_fold_change test_stat p_value q_value significant 1 TCONS_00246566 macrophage monocyte LOWDATA 0 0 -1.79769e+308 0 1 1 no
Code:
> fpkm(getFeatures(cuff,"TCONS_00246566")) isoform_id sample_name fpkm conf_hi conf_lo quant_status stdev 1 TCONS_00246566 macrophage 0.0000000 0.0000 0 LOWDATA 0.00000 2 TCONS_00246566 monocyte 0.0972739 49.0851 0 LOWDATA 24.49391
I know that csHeatmap() uses fpkm() to extract values for plotting, but which is the most accurate value?
I thought cuffdiff values (available from diffData()) were supposed to be the most accurate?