Please make sure your are using the "...gene_exp.diff" file that comes from CuffLinks. There are some applications that claim to emulate CuffDiff output (e.g. Galaxy). If you are using one of these applications, please make sure the output file has all columns populated. See below for specific columns that must be present. Also, use this link to view the Cuffdiff manual.
Column numberColumn nameExampleDescription 1Tested idXLOC_000001A unique identifier describing the transcipt, gene, primary transcript, or CDS being tested 2geneLypla1The gene_name(s) or gene_id(s) being tested 3locuschr1:4797771-4835363Genomic coordinates for easy browsing to the genes or transcripts being tested. 4sample 1LiverLabel (or number if no labels provided) of the first sample being tested 5sample 2BrainLabel (or number if no labels provided) of the second sample being tested 6Test statusNOTESTCan be one of OK (test successful), NOTEST (not enough alignments for testing), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents testing. 7FPKMx8.01089FPKM of the gene in sample x 8FPKMy8.551545FPKM of the gene in sample y 9log2(FPKMy/FPKMx)0.06531The (base 2) log of the fold change y/x 10test stat0.860902The value of the test statistic used to compute significance of the observed change in FPKM 11pvalue 0.389292The uncorrected p-value of the test statistic 12qvalue 0.985216The FDR-adjusted p-value of the test statistic 13significantnoCan be either “yes” or “no”, depending on whether p is greater then the FDR after Benjamini-Hochberg correction for multiple-testing