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
Tool: Cuffdiff
Tool: Cuffdiff
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
Created:
4-Apr-13
Created:
21-Aug-13
Filesize:
10.3 MB
Filesize:
10.2 MB
Dbkey:
hg19
Dbkey:
hg19
Format:
tabular
Format:
tabular
Galaxy Tool Version:
0.0.5
Galaxy Tool Version:
0.0.5
Tool Version:
Tool Version:
Tool Standard Output:
stdouthttps://main.g2.bx.psu.edu/datasets/bbd44e69cb8906b5355e4a035e92cd84/stdout
Tool Standard Output:
stdouthttps://main.g2.bx.psu.edu/datasets/bbd44e69cb8906b524bcf7e585f495b1/stdout
Tool Standard Error:
stderrhttps://main.g2.bx.psu.edu/datasets/bbd44e69cb8906b5355e4a035e92cd84/stderr
Tool Standard Error:
stderrhttps://main.g2.bx.psu.edu/datasets/bbd44e69cb8906b524bcf7e585f495b1/stderr
Tool Exit Code:
0
Tool Exit Code:
0
API ID:
bbd44e69cb8906b5355e4a035e92cd84
API ID:
bbd44e69cb8906b524bcf7e585f495b1
Input Parameter
Value
Note for rerun
Input Parameter
Value
Transcripts
261: Cuffmerge on data 258, data 135, and others: merged transcripts
Transcripts
261: Cuffmerge on data 258, data 135, and others: merged transcripts
Perform replicate analysis
Yes
Perform replicate analysis
Yes
Group name
s202
Group name
s202
Add file
194: Galaxy883-[MarkDups_Dupes_Marked_882_202.bam].bam
Add file
194: Galaxy883-[MarkDups_Dupes_Marked_882_202.bam].bam
Group name
Ctrls
Group name
Ctrls
Add file
236: MarkDups_Dupes Marked216.bam
Add file
236: MarkDups_Dupes Marked216.bam
Add file
225: MarkDups_Dupes Marked206.bam
Add file
225: MarkDups_Dupes Marked206.bam
Library normalization method
not used (parameter was added after this job was run)
Library normalization method
geometric
Dispersion estimation method
not used (parameter was added after this job was run)
Dispersion estimation method
pooled
False Discovery Rate
0.05
False Discovery Rate
0.05
Min Alignment Count
2
Min Alignment Count
2
Perform quartile normalization
No
Perform quartile normalization
No
Use multi-read correct
Yes
Use multi-read correct
Yes
Perform Bias Correction
Yes
Perform Bias Correction
Yes
Reference sequence data
cached
Reference sequence data
cached
Set Additional Parameters? (not recommended)
Yes
Set Additional Parameters? (not recommended)
Yes
Average Fragment Length
200
Average Fragment Length
200
Fragment Length Standard Deviation
80
Fragment Length Standard Deviation
80
..
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)
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