User: salamandra
salamandra • 170
- Reputation:
- 170
- Status:
- Trusted
- Location:
- Last seen:
- 22 hours ago
- Joined:
- 3 years, 2 months ago
- Email:
- t*************@gmail.com
Posts by salamandra
<prev
• 188 results •
page 1 of 19 •
next >
0
votes
2
answers
161
views
2
answers
... thank you very much! ...
written 27 days ago by
salamandra • 170
0
votes
2
answers
161
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 28 days ago by
salamandra • 170
0
votes
2
answers
161
views
2
answers
... 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 28 days ago by
salamandra • 170
4
votes
2
answers
161
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 28 days ago by
salamandra • 170
• updated
28 days ago by
exin • 30
0
votes
0
answers
163
views
0
answers
... 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 29 days ago by
salamandra • 170
0
votes
1
answer
185
views
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 4 weeks ago by
salamandra • 170
0
votes
1
answer
185
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 4 weeks ago by
salamandra • 170
0
votes
1
answer
185
views
1
answers
... And simply removing time of the table/design wouldn't be correct?
I ask because most of variance in PCA plot (PC1 and PC2) is due to cell type. Not even in PC2 and PC3 time seems to vary. ...
written 4 weeks ago by
salamandra • 170
0
votes
1
answer
185
views
1
answers
... I'm having problems in understanding confounding variables, because imagine this situation:
time <- factor(LETTERS[1:4])
celltype <- factor(c(1,2,2,3))
sampleNames <- c("hey","hi","HRY", "GT")
sampleFiles <- c("1A_ATCACG_counts", "2A_CAGATC_counts", "3A_ATCACG_counts", " ...
written 4 weeks ago by
salamandra • 170
1
vote
0
answers
160
views
0
answers
... I updated R to version 3.5 because I couldn't install package 'tibbles', but now the package I need the most 'DEseq2' is not installed. I tried to install with
source("https://bioconductor.org/biocLite.R")
biocLite()
biocLite("DESeq2")
and with
install.packages("DESeq2")
and i ...
written 4 weeks ago by
salamandra • 170
Latest awards to salamandra
Popular Question
1 day ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question
3 days ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Voter
4 weeks ago,
voted more than 100 times.
Popular Question
6 weeks ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: How to select a gene annotation file in ensembl that contain un-localized scaffo
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Centurion
12 weeks ago,
created 100 posts.
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Remove/Identify deprecated IDs from a list of Entrez IDs programatically
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
Supporter
10 months ago,
voted at least 25 times.
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
Student
15 months ago,
asked a question with at least 3 up-votes.
For Install DESeq2 and edgeR with Anaconda
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1401 users visited in the last hour