Hi all,
I have been trying out the new 1.3 version of the cufflinks package to see if the testing for differential splicing/expression etc is improved.
Now I expected a more stringent analysis, as announced, but I get mostly failed tests.
I used the same reads.bam and annotation and the same parameters (5 biological replicates and 2 groups, 2x 100 bp PE reads, ~ 140mil per sample).
This is my result with cuffdiff v1.0.3 for diff. promoter usage:
191 FAIL
13713 NOTEST
4745 OK
with 1403 Genes found with sign. diff. promoter usage.
Now this is the cuffdiff v 1.3 result:
5719 FAIL
35 LOWDATA
12301 NOTEST
594 OK
with 20 Genes found with sign. diff. promoter usage.
It seems that the number of false positives is really reduced. The new version find only ~ 3.5% of genes tested to be differential. However, so many fail to be tested in the first place that the result is not really usable.
Did anyone experience something similar? Is this failing of testing maybe related to my large dataset or the replicates?
All the best,
Sebastian
I have been trying out the new 1.3 version of the cufflinks package to see if the testing for differential splicing/expression etc is improved.
Now I expected a more stringent analysis, as announced, but I get mostly failed tests.
I used the same reads.bam and annotation and the same parameters (5 biological replicates and 2 groups, 2x 100 bp PE reads, ~ 140mil per sample).
This is my result with cuffdiff v1.0.3 for diff. promoter usage:
191 FAIL
13713 NOTEST
4745 OK
with 1403 Genes found with sign. diff. promoter usage.
Now this is the cuffdiff v 1.3 result:
5719 FAIL
35 LOWDATA
12301 NOTEST
594 OK
with 20 Genes found with sign. diff. promoter usage.
It seems that the number of false positives is really reduced. The new version find only ~ 3.5% of genes tested to be differential. However, so many fail to be tested in the first place that the result is not really usable.
Did anyone experience something similar? Is this failing of testing maybe related to my large dataset or the replicates?
All the best,
Sebastian
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