Question: "Significant" In Cuffdiff'S Ouput
0
Hoang, Thanh • 200 wrote:
Hi all,
I have some questions about how Cufffdiff does the statistical
analysis.
I am looking for DE genes in two sample groups ( 3 replicate per
group). In
the Cuffdiff;s gene_exp.diff, I found many genes that have very large
RPKM
fold-change between two groups (with p value < or > 0.05) but still
NO
significant. Something like this:
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
ENSMUSG00000047139
ENSMUSG00000047139 Cd24a 10:43579168-43584262 q1 q2 OK 96.2585 2700.55
4.8102 1.6486 0.03995 0.078237 no ENSMUSG00000066975
ENSMUSG00000066975
Cryba4 5:112246492-112252518 q1 q2 OK 424.582 46190.2 6.7654 0.598327
0.3408
0.442128 no
Then I checked the READ_GROUP_TRACKING file for those genes to check
the
RPKM value for each replicate:
tracking_id condition replicate raw_frags internal_scaled_frags
external_scaled_frags FPKM effective_length status ENSMUSG00000047139
q1 1
11256 5876.82 5876.82 125.915 - OK ENSMUSG00000047139 q1 0 3783
4343.44
4343.44 42.0316 - OK ENSMUSG00000047139 q1 2 10051 5639.48 5639.48
120.829
- OK ENSMUSG00000047139 q2 1 76771 156059 156059 3343.66 - OK
ENSMUSG00000047139 q2 0 82394 162172 162172 1420.33 - OK
ENSMUSG00000066975
q1 1 12825 6696 6696 407.899 - OK ENSMUSG00000066975 q1 0 3694
4241.26
4241.26 375.211 - OK ENSMUSG00000066975 q1 2 14397 8077.95 8077.95
490.636
- OK ENSMUSG00000066975 q2 1 348103 707619 707619 42455.1 - OK
ENSMUSG00000066975 q2 0 420896 828430 828430 48920.6 - OK
ENSMUSG00000066975 q2 2 331098 767405 767405 47195 - OK
Would not I expect these DE genes are significant? Could anyone
explain why
Cufflinks show this result?
Best regards
Thanh
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modified 5.4 years ago
by
Dave Clements ♦♦ 2.5k
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written
5.4 years ago by
Hoang, Thanh • 200