Portal Kombat : extension du réseau de propagande russe
Brendel Group Presentation: 17 Oct 2013
1. Differential expression in the paper
wasp Polistes dominula
Daniel S. Standage, Brendel Group Meeting, 17 Oct 2013
2. Experimental design
6 queen samples
6 worker samples
Queen x and worker x from same colony
(x ∈ [1 .. 6])
Hypothesis: identify handful of critical
caste-related genes/transcripts
3. Initial (naïve) analysis with RSEM/EBSeq
209,675 transcripts (assembled by Trinity)
RSEM and EBSeq completed without warnings
80-85% reads mapped
Many DE transcripts reported
5,769 (FDR=.05)
4,763 (FDR=.01)
3,878 (FDR=.001)
4. Permutation testing
Randomly shuffle caste labels (queen or worker)
Re-run differential expression analysis
Repeat test
Compare number of transcripts reported as DE for
each permutation
https://github.com/standage/dept
6. Some observations
Some expression levels very low
Some transcripts had very few reads mapped
Some transcripts had many read mapped
Difficulty normalizing over large dynamic range?
11. RSEM expected count
'expected_count' is the sum of the posterior
probability of each read comes from this transcript
over all reads. Because 1) each read aligning to this
transcript has a probability of being generated from
background noise; 2) RSEM may filter some
alignable low quality reads, the sum of expected
counts for all transcript are generally less than the
total number of reads aligned.
12. Next (final) steps
Look more into “expected count”
Additional filtering?
Publish!
![Experimental design
6 queen samples
6 worker samples
Queen x and worker x from same colony
(x ∈ [1 .. 6])
Hypothesis: identify handful of critical
caste-related genes/transcripts](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)