Hi All
I don't know whether somebody else has experience a similar problem.
I'm experiencing the following problem using the pre-compiled binary packages of Tophat-2.0.9 and Cufflinks-2.1.1 where Cuffdiff was reporting many genes and transcripts as having expression levels of zero or "nan" or "inf".
See output:
test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
XLOC_001554 XLOC_001554 - MDC001340.131:11788-12879 E0 E2 OK 10.7983 0 -inf nan 0.00025 0.0493497 yes
XLOC_001905 XLOC_001905 - MDC001635.618:38277-40655 E0 E2 OK 0 124.446 inf nan 5e-05 0.0183924 yes
XLOC_002511 XLOC_002511 - MDC002108.350:7225-9199 E0 E2 OK 0 32.3 inf nan 5e-05 0.0183924 yes
XLOC_003041 XLOC_003041 - MDC002536.231:5054-9739 E0 E2 OK 0 24.7014 inf nan 5e-05 0.0183924 yes
XLOC_003472 XLOC_003472 - MDC002955.278:7454-8285 E0 E2 OK 11.6936 0 -inf nan 0.00025 0.0493497 yes
XLOC_003551 XLOC_003551 - MDC003040.156:5-453 E0 E2 OK 117.279 0 -inf nan 0.0001 0.0300675 yes
XLOC_004619 XLOC_004619 - MDC004034.219:3633-4187 E0 E2 OK 64.2737 0 -inf nan 5e-05 0.0183924 yes
XLOC_005948 XLOC_005948 - MDC005198.374:10357-11692 E0 E2 OK 0 20.8865 inf nan 0.00025 0.0493497 yes
XLOC_006633 XLOC_006633 - MDC005799.555:2423-4474 E0 E2 OK 12.1785 0 -inf nan 0.00025 0.0493497 yes
XLOC_006750 XLOC_006750 - MDC005908.507:2483-3754 E0 E2 OK 19.815 0 -inf nan 0.0002 0.0446163 yes
Just a few of the DE_genes. See -inf and nan where I'm supposed to get value for log2(fold change). Any suggestions?
Thanks in advance.
Lizex
I don't know whether somebody else has experience a similar problem.
I'm experiencing the following problem using the pre-compiled binary packages of Tophat-2.0.9 and Cufflinks-2.1.1 where Cuffdiff was reporting many genes and transcripts as having expression levels of zero or "nan" or "inf".
See output:
test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
XLOC_001554 XLOC_001554 - MDC001340.131:11788-12879 E0 E2 OK 10.7983 0 -inf nan 0.00025 0.0493497 yes
XLOC_001905 XLOC_001905 - MDC001635.618:38277-40655 E0 E2 OK 0 124.446 inf nan 5e-05 0.0183924 yes
XLOC_002511 XLOC_002511 - MDC002108.350:7225-9199 E0 E2 OK 0 32.3 inf nan 5e-05 0.0183924 yes
XLOC_003041 XLOC_003041 - MDC002536.231:5054-9739 E0 E2 OK 0 24.7014 inf nan 5e-05 0.0183924 yes
XLOC_003472 XLOC_003472 - MDC002955.278:7454-8285 E0 E2 OK 11.6936 0 -inf nan 0.00025 0.0493497 yes
XLOC_003551 XLOC_003551 - MDC003040.156:5-453 E0 E2 OK 117.279 0 -inf nan 0.0001 0.0300675 yes
XLOC_004619 XLOC_004619 - MDC004034.219:3633-4187 E0 E2 OK 64.2737 0 -inf nan 5e-05 0.0183924 yes
XLOC_005948 XLOC_005948 - MDC005198.374:10357-11692 E0 E2 OK 0 20.8865 inf nan 0.00025 0.0493497 yes
XLOC_006633 XLOC_006633 - MDC005799.555:2423-4474 E0 E2 OK 12.1785 0 -inf nan 0.00025 0.0493497 yes
XLOC_006750 XLOC_006750 - MDC005908.507:2483-3754 E0 E2 OK 19.815 0 -inf nan 0.0002 0.0446163 yes
Just a few of the DE_genes. See -inf and nan where I'm supposed to get value for log2(fold change). Any suggestions?
Thanks in advance.
Lizex
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