User: Sib
Sib • 20
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Posts by Sib
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... Where are the method section and metadata? ...
written 3 months ago by
Sib • 20
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... No these are two different questions. I want to analyze microarray data in R. Now I want to know if I get the datasets by getGEO I should perform background correction and substitution of duplicates with the mean or like GEO2R not. ...
written 3 months ago by
Sib • 20
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... getGEO function is a way of getting datasets and their annotations from GEO in R when we want to analyze microarray data.
GEO2R uses this function to get datasets. I saw in the GEO2R scripts of many of GEO cases that the tool does not perform background correction and substitution of duplicates wit ...
written 3 months ago by
Sib • 20
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... Thanks for your answer. Can we say whenever we obtain datasets by using getGEO function, the data are background corrected and duplicates are substituted with mean, and even if we want to have our analyze by R (without GEO2R), if we get datasets through this function there is no need to background c ...
written 3 months ago by
Sib • 20
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... The commands below are the R scripts that are used to analyze my microarray data. I want to know which lines are responsible for
1-Replacing replicated probes with the mean
2-Background correction
# Differential expression analysis with limma
library(Biobase)
library(GEOquery)
...
written 3 months ago by
Sib • 20
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... I already have up-voted to the answer and ticked accept and after that, I deleted the post because I thought that it was not useful for the entire community. ...
written 3 months ago by
Sib • 20
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... I performed a differential expression analysis of microarray data. Now, I have a top table (tT) of results. The tT has logFC, adj.P.Val, GENE-SYMBOL columns. I want to plot a volcano plot by
EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
so I enter these co ...
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... thanks. I plotted a volcano plot by ggplot2 . the codes are as below:
ggplot(tT,aes(x=logFC,y=-log10(adj.P.Val)))+geom_point()
Now, I want to change the colors of genes with |logFC|>2 and adj-P-Val<0.05. And I want to show their gene-symbols. What codes I should add to ggplots codes? ...
written 3 months ago by
Sib • 20
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... thanks for answering. I will be appreciated more if you write the codes that I should use for doing this.
...
written 3 months ago by
Sib • 20
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