User: mccallionc403

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Posts by mccallionc403

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Answer: A: Volcano plot labeling troubles
... Thank you so much ...
written 3.1 years ago by mccallionc4030
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Volcano plot labeling troubles
... Hello, I am trying to make a volcano plot, but of Log Fold Change vs FDR adjusted p-values.  So far, I've managed to make a decent plot, but I'm having trouble figuring out how to label the genes that are differentially expressed, wether as the top, say 30, genes, or all of the genes above a certai ...
limma volcanoplot written 3.1 years ago by mccallionc4030 • updated 3 months ago by Gordon Smyth32k
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Comment: C: Are the p-values supposed to be on the order of 10^-120?
... I do apologize.  I made a typo.  However, in the line: IsExpressed <- fit$Amean>3 I would think that that means that a gene is considered to be expressed if the average expression value is greater than 3.  Why does this have to be greater than 3? ...
written 3.1 years ago by mccallionc4030
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Comment: C: Are the p-values supposed to be on the order of 10^-120?
... Okay.  Possibly obvious question:  How would I go about doing that, or where would I start at least? ...
written 3.1 years ago by mccallionc4030
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Comment: C: Are the p-values supposed to be on the order of 10^-120?
... Thank you.  I updated my software.  However, I still get the following error message: Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim, : No residual degrees of freedom in linear model fits In addition: Warning messages: 1: installed directory not writable, c ...
written 3.1 years ago by mccallionc4030
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Comment: C: Are the p-values supposed to be on the order of 10^-120?
... Okay, but then how do I know which genes have significant fold changes if the P.Values are so small? ...
written 3.1 years ago by mccallionc4030
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Comment: C: Are the p-values supposed to be on the order of 10^-120?
... Additionally, when I run your code, I get the following error: Error in eBayes(fit[IsExpressed, ], trend = TRUE, robust = TRUE) : Need Amean component in fit to estimate trend In addition: Warning messages: 1: installed directory not writable, cannot update packages 'boot', 'class', 'cluster' ...
written 3.1 years ago by mccallionc4030
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Comment: C: Are the p-values supposed to be on the order of 10^-120?
... Thank you so much.  However, I notice that your code would still give constant adj.P.Vals ...
written 3.1 years ago by mccallionc4030
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Comment: C: Are the p-values supposed to be on the order of 10^-120?
... Forgot to put in the commands and such the commands: source("http://bioconductor.org/biocLite.R") biocLite() biocLite("limma") biocLite("GEOquery") library("limma") library("GEOquery") #gds4523 <- getGEO("GDS4523") #eset4523 <- GDS2eSet(gds4523) gse17612 <- getGEO("GSE17612", GSEMatri ...
written 3.1 years ago by mccallionc4030
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Are the p-values supposed to be on the order of 10^-120?
... I have been working on a project for a while now.  For my data, I have tried converting the GDS file into an eSet object, fitting it with lmFit, from the limma package (with and without a design matrix as a parameter), and getting a hold of the raw CEL files, running those through justRMA, from the ...
affy limma bioconductor affymetrix written 3.1 years ago by mccallionc4030 • updated 3.1 years ago by Gordon Smyth32k

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Popular Question 3.0 years ago, created a question with more than 1,000 views. For Volcano plot labeling troubles

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