User: Sib

gravatar for Sib
Sib20
Reputation:
20
Status:
New User
Location:
Last seen:
3 weeks, 3 days ago
Joined:
3 months, 3 weeks ago
Email:
m*************@yahoo.com

Posts by Sib

<prev • 38 results • page 1 of 4 • next >
0
votes
1
answer
152
views
1
answers
Comment: C: Is there a need for background correction and substitution of duplicates with th
... Where are the method section and metadata? ...
written 3 months ago by Sib20
0
votes
1
answer
152
views
1
answers
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 3 months ago by Sib20
0
votes
1
answer
152
views
1
answer
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 3 months ago by Sib20
0
votes
2
answers
233
views
2
answers
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 3 months ago by Sib20
7
votes
2
answers
233
views
2
answers
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 3 months ago by Sib20
0
votes
1
answer
203
views
1
answers
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 3 months ago by Sib20
0
votes
1
answer
203
views
1
answers
Comment: C: Error in plotting Enhanced Volcano plot
... Thanks for answering. ...
written 3 months ago by Sib20
2
votes
1
answer
203
views
1
answer
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 3 months ago by Sib20 • updated 3 months ago by dsull1.0k
0
votes
0
answers
198
views
0
answers
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 3 months ago by Sib20
0
votes
0
answers
198
views
0
answers
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 3 months ago by Sib20

Latest awards to Sib

Supporter 3 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1139 users visited in the last hour