User: Leite
Leite • 950
- Reputation:
- 950
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- Location:
- São Paulo - Brazil - Unifesp
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- Google Scholar Page
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- 23 hours ago
- Joined:
- 3 years, 6 months ago
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Posts by Leite
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Comment:
C: Collapsed to unique genes
... Hey russhh,
Yes it's an ExpressionSet.
Maybe I found the answer:
class(fil_eset_NA3) <- "numeric"
is.numeric(fil_eset_NA3)
TRUE ...
written 12 weeks ago by
Leite • 950
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... Hello everyone,
I've a problem with gene expression analysis. I found a [similar post][1] that I used as a guide, but could not solve my problem.
First I downloaded the normalized file directly from GEO. Then, I download the annotation file containing the probe name for gene name and use the `mer ...
written 12 weeks ago by
Leite • 950
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... Dear anna
You can try [ESCHER][1] and [MetaboAnalyst][2]
[1]: https://escher.github.io/
[2]: https://www.metaboanalyst.ca/ ...
written 4 months ago by
Leite • 950
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Answer:
A: Trainning on NGS
... Dear @jahanshanzida
I recently updated a bioinformatics curriculum where you can find a number of NGS-related courses.
https://www.biostars.org/p/405248/
With regard to book, there is Biostar Handbook which is a good start in NGS.
https://www.biostars.org/p/225812/
Best,
Leite ...
written 4 months ago by
Leite • 950
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... Dear @F. Golestan
>1. generate your network in string db using your list of genes or proteins as shown in **figure 1**.
**Figure 1.**
>2. Make sure the string list is the same as the list you entered, then proceed **Figure 2**
**Figure 2**
>3.Select your parameters **Figure 3**
...
written 4 months ago by
Leite • 950
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... Dear @ F. Golestan
I think part of your question is being discussed [here][1] and there is no need for a new question!!!
https://www.biostars.org/p/406796/#406869
[1]: https://www.biostars.org/p/406796/#406869 ...
written 4 months ago by
Leite • 950
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... Dear @F. Golestan,
Many questions, I will try to answer all.
> First question:
I commonly use [STRING db][1], and there I put my parameters as Interactions experimentally determined or from curated databases with a minimum interaction score of 0.400. Then I export txt and import it into cytos ...
written 4 months ago by
Leite • 950
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Comment:
C: normalization of Agilent data
... Add the code you are using, this may help us to find the possible error. ...
written 4 months ago by
Leite • 950
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... Dear @F. Golestan
From my experience working with network (PPIN), I advise you to import data from [cytoscape][1] so you will have more flexibility to work by changing colors, font size, node color and whatever you want to change your layout.
With regards to DAVID, you can download GO result and b ...
written 4 months ago by
Leite • 950
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... @Ali
To process 19k interactions in cytoscape, you would have to have a super computer.
Another point, your network would be unreadable.
You need to put a weight filter for interactions, then import into cytoscape.
Get only the links with a weight higher than some threshold
>"Alternatively, a ...
written 4 months ago by
Leite • 950
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