User: elb
elb • 150
- Reputation:
- 150
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- Torino
- Last seen:
- 2 days, 23 hours ago
- Joined:
- 6 years, 3 months ago
- Email:
- l****************@gmail.com
about me
Posts by elb
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Comment:
C: log transformation of rpkm
... Thank you Kevin! You help me a lot every time! Thank you again! ...
written 22 days ago by
elb • 150
10
votes
2
answers
147
views
6 follow
2
answers
... Hi guys, I have a question about how to define a gene to be expressed in RNA Seq analysis.
Is it better to use log2(rpkm) or rpkm without log2 transformation to define a gene to be expressed? I know that the log is only a transformation so that log2(rpkm) will let to consider as expressed a gene wit ...
written 22 days ago by
elb • 150
• updated
21 days ago by
Charles Warden ♦ 5.6k
1
vote
1
answer
141
views
1
answers
... Thank you Kevin for your answer. I simply normalized my data and then performed an unsupervised HCA with Pearson correlation as a measure of distance. I have no reference samples. Then the clusters appeared. I appreciate a lot your work. I think I could be inspired by it. Thank you a lot.
...
written 27 days ago by
elb • 150
0
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0
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93
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0
answers
... Oh God. I think I had a problem with the internet connection. Is there a way to remove one of the questions? ...
written 27 days ago by
elb • 150
0
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0
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93
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0
answers
... Hi guys,
I have a big data.frame of RNA-Seq counts in which rows are genes while columns are samples.
I clustered this big matrix and I identified 6 major clusters. They have some common genes, i.e. genes that do not show a huge variation between the samples (around 100 patients) and some genes th ...
3
votes
1
answer
141
views
1
answer
... Hi guys,
I have a big data.frame of RNA-Seq counts in which rows are genes while columns are samples.
I clustered this big matrix and I identified 6 major clusters. They have some common genes, i.e. genes that do not show a huge variation between the samples (around 100 patients) and some genes th ...
written 28 days ago by
elb • 150
• updated
27 days ago by
Kevin Blighe ♦ 31k
2
votes
0
answers
149
views
5 follow
0
answers
... Hi guys,
I'm trying to analyse some beadchip data from here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32025. I would like to select genes that are expressed according to the "Detection p-value" criteria. However, this information is not present neither in raw-data nor in the normalized ...
written 4 weeks ago by
elb • 150
1
vote
0
answers
92
views
5 follow
0
answers
... Hi guys,
I have a question about the normalization of RNA Seq data. I have 3 types of cells of which I would like to identify the differentially expressed genes. As reported in many papers and tutorials, data have to be normalized together. However, I'm afraid that the normalisation could affect t ...
written 5 weeks ago by
elb • 150
• updated
5 weeks ago by
WouterDeCoster ♦ 34k
3
votes
1
answer
100
views
5 follow
1
answer
... Hi guys,
is there someone who can explain me the meaning of the sva output as from the sva R library?
In other words I run svobj = sva(edata,mod,mod0,n.sv=n.sv) as here https://www.bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf but it is not clear to me the meaning of the th ...
written 6 weeks ago by
elb • 150
• updated
6 weeks ago by
Devon Ryan ♦ 86k
1
vote
1
answer
125
views
1
answers
... Thank you very much Kevin! ...
written 7 weeks ago by
elb • 150
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