User: Leite
Leite • 300
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Posts by Leite
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Comment:
C: Gene expression using R
... Dear jrj.healey,
Thank you for the reply and sorry for the mistake.
I think my best option will be a new machine. ...
written 11 weeks ago by
Leite • 300
0
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Comment:
C: Gene expression using R
... Sorry, I made a mistake, yes it's 6GB and not 6MB ...
written 11 weeks ago by
Leite • 300
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Comment:
C: Gene expression using R
... Dear jrj.healey,
6Mb is the total memory capacity of my computer. ...
written 11 weeks ago by
Leite • 300
3
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1
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6 follow
1
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... Hello everyone,
I am analyzing a large microarray database, (n = 820), And the R has reached the total memory of my computer
Warning messages:
1: In dimnames(object[[nm]]) <- dn :
Reached total allocation of 6036Mb: see help(memory.size)
2: In dimnames(object[[nm]]) <- ...
written 11 weeks ago by
Leite • 300
• updated
11 weeks ago by
Santosh Anand • 4.0k
1
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141
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1
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... Thank you so much my friend! ...
written 3 months ago by
Leite • 300
4
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1
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... Hello everyone,
I have a simple question, the file `series_matrix.txt` in GEO are always the normalized data of the study?
Best,
Leite ...
written 3 months ago by
Leite • 300
• updated
3 months ago by
Kevin Blighe ♦ 30k
1
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1
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617
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... Dear krushnach80,
In our study, we did not use the "TTN" sequence as seed but rather the gene itself.
And yes, just put the name of the gene of interest in BIOGRID as well as in the other databases and find the interactions. ...
written 3 months ago by
Leite • 300
2
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1
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617
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... Dear krushnach,
With regard to the parameters to filter the key nodes of the network, they come according to the number of nodes and vertices of the network. If you have a large network, you put a high degree, BC and the CC, and the same if it is a small network, you can put a smaller cut-off.
Fo ...
written 3 months ago by
Leite • 300
1
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0
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305
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... Oi Kevin,
This point I had not thought of.
"The only other thing that you need to ensure is that your column names (in `eset`) are in the same order as your samples in `targets`."
Thank you very much for this super tip, it made all the difference now. ...
written 4 months ago by
Leite • 300
0
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... Boa tarde Kevin,
I can find many genes with an adjusted p <0.05. I'll try what you mentioned.
What does not make me very comfortable with this code is this function `eset <- readExpressionSet` I'm still studying more about it.
...
written 4 months ago by
Leite • 300
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