User: salamandra
salamandra • 170
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Posts by salamandra
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Comment:
C: BioMart: connection fails
... Yes, from the links seems to be working and when I was one other computer (mac) it doesn't give an error, but when I use this computer (windows) it doesn't work. Could be some problem with package version? I tried to install same package version on both without success. ...
written 2 days ago by
salamandra • 170
0
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2
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368
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2
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Comment:
C: BioMart: connection fails
... Hi, now it's not working again. With
> useast.ensembl.org
>
> uswest.ensembl.org
and even if I run:
listMarts()
get the error:
Request to BioMart web service failed. The BioMart web service you're
accessing may be down. Check the following URL and see if this website
...
written 3 days ago by
salamandra • 170
0
votes
2
answers
368
views
2
answers
Comment:
A: BioMart: connection fails
... Hi, now it's not working again. With
> useast.ensembl.org
> uswest.ensembl.org
and even if I run:
> listMarts()
get the error:
Request to BioMart web service failed. The BioMart web service you're
accessing may be down. Check the following URL and see if this website
...
written 3 days ago by
salamandra • 170
0
votes
2
answers
228
views
2
answers
... thank you very much! ...
written 11 weeks ago by
salamandra • 170
0
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2
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228
views
2
answers
... You're talking about distance matrix? I know I can use to visualize those groups in a heatmap, but then how to aftwrwards automatically get the list of genes in each group/branch separately? I have a lot of genes so cannot do it manually ...
written 11 weeks ago by
salamandra • 170
0
votes
2
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228
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2
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... Yes, the thing is to know which genes are in the same group. Each plot shows a group of genes with the same behaviour through time ...
written 11 weeks ago by
salamandra • 170
4
votes
2
answers
228
views
6 follow
2
answers
... Does anyone know of a tool that can produce similar plots to 'DegPatterns' function of 'DEGreport' R package?
something like this [plot][1]? Basically is a plot showing how groups of genes change over time.
Cause I'm having difficulties with DegPatterns.
[1]: https://github.com/hbctraining/DGE ...
written 11 weeks ago by
salamandra • 170
• updated
11 weeks ago by
exin • 30
0
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0
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230
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... When running this:
clusters <- degPatterns(cluster_rlog, metadata = TableBJ, time = "condition", col=NULL)
I get this error:
Error in lower.to.upper.tri.inds(n) : 'n' must be >= 2
and also get a warning:
Large number of genes given. Please,make sure is not an error. NormallyOn ...
written 12 weeks ago by
salamandra • 170
0
votes
1
answer
263
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1
answers
... thank you :)
I'm not sure, as I haven't done it.
I'll just play safe and work with each combination of time and celltype, intead of time alone or cell type alone ...
written 12 weeks ago by
salamandra • 170
0
votes
1
answer
263
views
1
answers
... The experience consists in converting one cell type in the other. So, at different time points of the process we did rna_seq. Celltype is the phenotype we observed. So for one of the time points we observed two phenotypes and variance was big and for two other time points which shared same phenotype ...
written 12 weeks ago by
salamandra • 170
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