User: elb
elb • 160
- Reputation:
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- Torino
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Posts by elb
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131
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answers
... Hi guys, I know it could be an answer 1000 times redundant but I looked around without find a quick solution. I have 5 .bam files and a .gtf file that looks like this:
> 1 134202951 134202953
> 1 134202954 134203590
> 1 134199215 134203590
where 1 indicates ch ...
written 29 days ago by
elb • 160
0
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1
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149
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1
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... Yes I know! My problem is that my samples are highly variable but as you correctly say the cross comparison of results could be affected if samples are considered in a "paired" analysis. ...
written 5 weeks ago by
elb • 160
0
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1
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149
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1
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... Ohhhh wow! The answer I was looking for! Thank you very much. EdgeR does not address this point! Thank you very much! ...
written 5 weeks ago by
elb • 160
0
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... Thank you very much! I have another doubt. The estimateDisp should be done on the entire count matrix or on the subset of comparisons you want to look at? For example considering only samples in Treatment1 end Control1 on all the samples together? My point is: if you do not compare the Treatments ac ...
written 5 weeks ago by
elb • 160
0
votes
1
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149
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... No and this is why I'm asking because of some doubts
...
written 5 weeks ago by
elb • 160
2
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1
answer
149
views
5 follow
1
answer
... Hi guys,
suppose to have the following situation:
> MouseA MouseB MouseC
> Treatment1 Treatment1 Treatment1
> Control1 Control1 Control1
> Treatment2 Treatment2 Treatment2
> Cont ...
2
votes
1
answer
110
views
1
answer
... Hi guys,
I have a general question regarding the pre-ranked GSEA.
I have a list of genes ranked according to the LogFC and then a list of genes that is my geneset.
I would like to see if the genes of the geneset are enriched in my ranked list. To do this,
I'm running the pre-ranked GSEA. I'm no ...
4
votes
1
answer
204
views
1
answer
... Hi guys,
suppose to be in the following situation:
SampleA1 SampleA2 SampleA3 Ctrl1 Ctrl2 SampleB1 SampleB2 SampleB3
234 1 32 5 2 0 21 12344
2434 134 0 2 0 0 0 ...
2
votes
0
answers
160
views
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answers
... Hi guys,
I have a general question regarding the correct use of estimateDisp function of edgeR.
Suppose you have the following situation:
Sample Condition
A1 Control
A2 Control
B1 Treatment1
B2 Treatment1
B3 Treatment1
...
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