Entering edit mode
7.5 years ago
bdiciac2
•
0
I was using the tuxedo package to analyze RNAseq data. Tophat to map reads, cufflinks to estimate abundances, cuffmerge to merge files, and cuffdiff to determine DEGs. I have several questions on the cuffdiff output, in which I used version 2.2.1
#gene.exp output
gene sample_1 sample_2 status value_1 value_2 log2.fold_change. test_stat p_value q_value
Osm6 Kc167_NT60 Kc167_XR60 OK 11.0958 10.967 -0.016852 -0.00819555 0.0163 0.91993
CG4297 Kc167_NT60 Kc167_XR60 OK 3.28251 13.4614 2.03596 0.197429 0.0367 0.91993
Mst57Db Kc167_NT60 Kc167_XR60 OK 0 6.35973 Inf NA 0.0084 0.91993
snoRNA:CG16892-a Kc167_NT60 Kc167_XR60 OK 0 18.2782 Inf NA 0.02785 0.91993
#Replicate FPKM Values for gene Osm6 (from genes.read_group_tracking)
gene condition replicate raw_frags internal_scaled_frags external_scaled_frags FPKM effective_length status
Osm6 Kc167_NT60 0 296 289.701 289.701 8.75187 - OK
Osm6 Kc167_NT60 1 529 467.688 467.688 13.4397 - OK
Osm6 Kc167_XR60 0 268 285.888 285.888 8.43789 - OK
Osm6 Kc167_XR60 1 441 471.429 471.429 13.496 - OK
- Why does gene Osm6 give a p-value of 0.02 even though the magnitude of the test statistic is very small and the FPKM values between treatments are almost identical (11.10 vs 10.97)? I would have expected a much larger p-value.
- How is a p_value calculated for genes with "NA" test statistics?
Thank you