User: Sib

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Sib20
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Posts by Sib

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Is there a need for background correction and substitution of duplicates with th
... Where are the method section and metadata? ...
written 18 days ago by Sib20
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Comment: C: Is there a need for background correction and substitution of duplicates with th
... 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 18 days ago by Sib20
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Is there a need for background correction and substitution of duplicates with the mean when we use the getGEO function of R in microarray analysis?
... 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 ...
geo R microarray analysis written 18 days ago by Sib20
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Comment: C: In R scripts of GEO2R which line is responsible for background correction and re
... 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 19 days ago by Sib20
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In R scripts of GEO2R which line is responsible for background correction and replacing replicated probes with the mean?
... 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) ...
R differential expression analysis written 20 days ago by Sib20
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Comment: C: Error in plotting Enhanced Volcano plot
... 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 26 days ago by Sib20
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Comment: C: Error in plotting Enhanced Volcano plot
... Thanks for answering. ...
written 26 days ago by Sib20
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Error in plotting Enhanced Volcano plot
... 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 ...
differential expression analysis enhanced volcano written 26 days ago by Sib20 • updated 26 days ago by dsull830
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Comment: C: Error in volcano plot drawing with R.
... 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 27 days ago by Sib20
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Comment: C: Error in volcano plot drawing with R.
... thanks for answering. I will be appreciated more if you write the codes that I should use for doing this. ...
written 27 days ago by Sib20

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Supporter 26 days ago, voted at least 25 times.

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