User: Sib

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Sib20
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Posts by Sib

<prev • 42 results • page 2 of 5 • next >
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Comment: C: Error in plotting Enhanced Volcano plot
... Thanks for answering. ...
written 11 months 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 11 months ago by Sib20 • updated 11 months ago by dsull1.6k
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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 11 months 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 11 months ago by Sib20
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Comment: C: Error in volcano plot drawing with R.
... In fit object, there are no p-values ...
written 11 months ago by Sib20
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Comment: C: Error in volcano plot drawing with R.
... I am new to this analysis and I don't know whether It should have p-value or not But when I call fit, the results are these: > fit An object of class "MArrayLM" $coefficients Normal Tumor A_19_P00315452 7.134198 6.256601 A_19_P00315459 6.925040 7.04657 ...
written 11 months ago by Sib20
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Error in volcano plot drawing with R.
... I want to draw a volcano plot. I don't know where I make a mistake that I get an error. These are the codes: library(Biobase) library(GEOquery) library(ggplot2) library(pheatmap) library(limma) library(plyr) gset<-getGEO("GSE116959",GSEMatrix = TRUE,AnnotGPL = TRUE,de ...
R written 11 months ago by Sib20 • updated 6 weeks ago by Gordon Smyth2.0k
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Comment: C: After differential expression analysis if we use gene symbols for further analys
... It is an identifier. I think its complete name is HGNC-GENE-SYMBOl. ...
written 11 months ago by Sib20
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Comment: C: String db knows some gene symbols of DEGs for more than one protein and after e
... thanks to reply my question. I also have tried ensemble IDs. But the same problem occurs is about ensemble IDs. I saw in many related articles researchers used GENE-SYMBOLs for transferring genes from GEO to STRING and I was wondering about that because they lose many DEGs. ...
written 11 months ago by Sib20
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Comment: C: After differential expression analysis if we use gene symbols for further analys
... thank you for answering. Sorry, I think I explained badly. My meaning of DEG symbols was GEN_SYMBOLs of DEGs. In other words I have a list of DEGs in GENE_SYMBOl format. ...
written 11 months ago by Sib20

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Popular Question 5 months ago, created a question with more than 1,000 views. For How can I put the Rtools on PATH?
Supporter 11 months ago, voted at least 25 times.

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