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  • cummeRbund diffData() or fpkm() values

    I'm getting different FPKM values from diffData() and fpkm() on a couple of different isoform IDs

    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
    diffData() reports an fpkm of 0 for sample_2 (reported as "value_2")

    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
    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?

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