Hi,
I am wondering why Cuffdiff suddenly gives many more significant DE genes?
I have used same input data and now get approx 5x more significant genes, settings is same with the exception that you now included library normalization and dispersion estimation. See below for parameters.
I have rerun several analysis, also with more samples in each group, all give much more significant genes. Why?
Also, will replicate information soon be included in output files?
Kind regards,
Johanna
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Tool: Cuffdiff |
Tool: Cuffdiff |
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Name: |
Cuffdiff on data 225, data 236, and others: splicing differential expression testing |
Name: |
Cuffdiff on data 225, data 236, and others: splicing differential expression testing |
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Created: |
4-Apr-13 |
Created: |
21-Aug-13 |
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Filesize: |
10.3 MB |
Filesize: |
10.2 MB |
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Dbkey: |
hg19 |
Dbkey: |
hg19 |
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Format: |
tabular |
Format: |
tabular |
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Galaxy Tool Version: |
0.0.5 |
Galaxy Tool Version: |
0.0.5 |
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Tool Version: |
Tool Version: |
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Tool Standard Output: |
Tool Standard Output: |
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Tool Standard Error: |
Tool Standard Error: |
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Tool Exit Code: |
0 |
Tool Exit Code: |
0 |
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API ID: |
bbd44e69cb8906b5355e4a035e92cd84 |
API ID: |
bbd44e69cb8906b524bcf7e585f495b1 |
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Input Parameter |
Value |
Note for rerun |
Input Parameter |
Value |
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Transcripts |
261: Cuffmerge on data 258, data 135, and others: merged transcripts |
Transcripts |
261: Cuffmerge on data 258, data 135, and others: merged transcripts |
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Perform replicate analysis |
Yes |
Perform replicate analysis |
Yes |
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Group name |
s202 |
Group name |
s202 |
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Add file |
194: Galaxy883-[MarkDups_Dupes_Marked_882_202.bam].bam |
Add file |
194: Galaxy883-[MarkDups_Dupes_Marked_882_202.bam].bam |
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Group name |
Ctrls |
Group name |
Ctrls |
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Add file |
236: MarkDups_Dupes Marked216.bam |
Add file |
236: MarkDups_Dupes Marked216.bam |
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Add file |
225: MarkDups_Dupes Marked206.bam |
Add file |
225: MarkDups_Dupes Marked206.bam |
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Library normalization method |
not used (parameter was added after this job was run) |
Library normalization method |
geometric |
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Dispersion estimation method |
not used (parameter was added after this job was run) |
Dispersion estimation method |
pooled |
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False Discovery Rate |
0.05 |
False Discovery Rate |
0.05 |
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Min Alignment Count |
2 |
Min Alignment Count |
2 |
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Perform quartile normalization |
No |
Perform quartile normalization |
No |
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Use multi-read correct |
Yes |
Use multi-read correct |
Yes |
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Perform Bias Correction |
Yes |
Perform Bias Correction |
Yes |
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Reference sequence data |
cached |
Reference sequence data |
cached |
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Set Additional Parameters? (not recommended) |
Yes |
Set Additional Parameters? (not recommended) |
Yes |
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Average Fragment Length |
200 |
Average Fragment Length |
200 |
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Fragment Length Standard Deviation |
80 |
Fragment Length Standard Deviation |
80 |
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......................................................................................................................................................
Johanna Sandgren, PhD
Department of Oncology-Pathology
CCK, Karolinska Institutet
SE-171 76 Stockholm, Sweden
+46-8-517 721 35 (office),
+46-8- 321047(fax), +46-708 388476 (mobile)