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 number | Column name | Example | Description |
|---|---|---|---|
| 1 | Tested id | XLOC_000001 | A unique identifier describing the transcipt, gene, primary transcript, or CDS being tested |
| 2 | gene | Lypla1 | The gene_name(s) or gene_id(s) being tested |
| 3 | locus | chr1:4797771-4835363 | Genomic coordinates for easy browsing to the genes or transcripts being tested. |
| 4 | sample 1 | Liver | Label (or number if no labels provided) of the first sample being tested |
| 5 | sample 2 | Brain | Label (or number if no labels provided) of the second sample being tested |
| 6 | Test status | NOTEST | Can 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. |
| 7 | FPKMx | 8.01089 | FPKM of the gene in sample x |
| 8 | FPKMy | 8.551545 | FPKM of the gene in sample y |
| 9 | log2(FPKMy/FPKMx) | 0.06531 | The (base 2) log of the fold change y/x |
| 10 | test stat | 0.860902 | The value of the test statistic used to compute significance of the observed change in FPKM |
| 11 | p | value 0.389292 | The uncorrected p-value of the test statistic |
| 12 | q | value 0.985216 | The FDR-adjusted p-value of the test statistic |
| 13 | significant | no | Can be either “yes” or “no”, depending on whether p is greater then the FDR after Benjamini-Hochberg correction for multiple-testing |