cuffdiff: part of a cuffdiff analysis
In psikon/cuffgo: cufflinks and GO analysis

Description Usage Format References

This data set give the first 1000 lines of a RNA-Seq experiment in human B lymphoma cells. The cufflinks suite was used to assemble the transcripts and search for differenly expressed genes. For the identification of the transcripts and exons the Ensembl annotations were used.

1	data(cuffdiff)

A data frame with 999 observations on the following 16 variables from a cuffdiff (V2.0) run:

test_id: A unique identifier describing the gene being tested.
gene_id: The gene_name or gene_id
gene: The gene_name(s) or gene_id(s) being tested
locus: Genomic coordinates for easy browsing to the genes or transcripts being tested.
sample_1: Label (or number if no labels provided) of the first sample being tested
sample_2: Label (or number if no labels provided) of the second sample being tested
status: 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.
value_1: FPKM of the gene in sample x
value_2: FPKM of the gene in sample y
log2.fold_change.: The (base 2) log of the fold change y/x
test_stat: The value of the test statistic used to compute significance of the observed change in FPKM
p_value: The uncorrected p-value of the test statistic
q_value: The FDR-adjusted p-value of the test statistic
significant: Can be either "yes" or "no", depending on whether p is greater then the FDR after Benjamini-Hochberg correction for multiple-testing