I am using cuffdiff to perform differential expression analysis on RNA seq data. We have two conditions, each having three replicates. Our pipeline completes successfully and the data seems sane, however there is one anomaly which we are still wondering about...
Here is an example:
gene locus status value_1 value_2 log2(fold_change) test_stat p_value q_value significant SNORD111B chr16:70557690-70611571 NOTEST 0 4114.4 inf 0 1 1 no
There is 0 expression in condition 1 but very high expression in condition 2, but this was called as NOTEST and marked as non-significant. Why is this the case?