User: sabaghianamir70
sabaghianamir70 • 10
- Reputation:
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- Location:
- iran
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- 3 weeks, 5 days ago
- Joined:
- 1 year, 3 months ago
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Phd student in molecular medicine
Posts by sabaghianamir70
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Comment:
C: Differential expression issue
... How can i check that ? I almost tried every option in edgR or Deseq2. can you explain how can i control the different baseline expression level ? ...
written 6 weeks ago by
sabaghianamir70 • 10
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C: Differential expression issue
... ![enter image description here][1]
[1]: http://uupload.ir/files/9o25_bio_2.png
As you can see in this picture, All p value adj are above the 0.05 ...
written 6 weeks ago by
sabaghianamir70 • 10
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C: Differential expression issue
... ![enter image description here][1]
[1]: http://uupload.ir/files/ucjm_bio.png
this is how i set up my analysis..each Count file includes 5 time points. ...
written 6 weeks ago by
sabaghianamir70 • 10
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C: Differential expression issue
... because I should pay for using cloud services, i just trying to test the whole thing in galaxy. If it helping, i can just send all workflow here.
Rscript '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/edger/334ce9b1bac5/edger/edger.R' -R '/data/dnb02/galaxy_db/job_working_directory/0 ...
written 6 weeks ago by
sabaghianamir70 • 10
• updated
6 weeks ago by
RamRS ♦ 26k
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C: Differential expression issue
... I have 5 patients which all have 5 timepoints.(0 1 3 5 7)
So i just need to take all samples which belongs to time 0, and compare them to other time points
For example : 0-1 0-3 0-5 0-7
The main issue is about my FDR and p value adj, because in when i run it with edgeR, i have no significant ...
written 6 weeks ago by
sabaghianamir70 • 10
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Comment:
C: Differential expression issue
... Deseq and edgeR. i tried both.
As i said : I thought i can compare all time 0 from 5 patients to all time 1. ...
written 6 weeks ago by
sabaghianamir70 • 10
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... Hello
I having a problem with analyzing my data..
I have 5 time points of 5 patients, So the problem is, when i take all timepoints 0 from all patients and compare them with timepoints 1 from all patients, my p value adj failed.
P.s i cant compare each person separately, because i just have one sa ...
written 6 weeks ago by
sabaghianamir70 • 10
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... Do you approve this method ? https://www.biostars.org/p/414790/#414823 (benformatics said) ...
written 3 months ago by
sabaghianamir70 • 10
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... I did that said, it seems everything is fine, So @ATpoint and @genomax, Do you approve this method ? ...
written 3 months ago by
sabaghianamir70 • 10
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... Im using bowtie2, also i can use RNA STAR(which is not preferable), and Hisat2. i cant use bowtie v1. is there any other tool which i can use ?
in Bowtie2, i did convert to RNA but still no result. ...
written 3 months ago by
sabaghianamir70 • 10
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