Question

DGE analysis with LIMMA

0

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Amit • 0

@b648b3f5

Last seen 6 months ago

India

# DGE Analysis with Limma.
# Model matrix.
design <- model.matrix(~0+PHENO$Group)
fit <- lmFit(VAR.exprs, design)
contrasts <- makeContrasts(G3- G1, G3 - G2, G1 - G2, levels=design)
fit2 <- contrasts.fit(fit, contrasts)
fit2 <- eBayes(fit2)
#Results
topTable(fit2)
decideTests(fit2)
table(decideTests(fit2))
Results <- decideTests(fit2)
summary(Results)
## Venn Diagram
vennDiagram(Results)

The vennDiagram shows common genes. How would i extract those with all there details like logfc, p value, adj.p.value and so on in a table.

limma • 901 views

ADD COMMENT • link updated 9 months ago by Gordon Smyth 52k • written 9 months ago by Amit • 0

score 2 · Answer 1 · 2024-03-01

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 1 day ago

United States

The Results object is a matrix with -1 or 1 if a given gene is significant, so rowSums(abs(Results)) == 3L will give you all the genes that are in the intersection. You can then use topTable (with sort.by = "none"), and the indicator variable generated using rowSums to subset to the genes in the intersection for each contrast, and then merge as you see fit.

ADD COMMENT • link 9 months ago James W. MacDonald 67k

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Thanks James, but can you please share script/code as i am new in this field.

ADD REPLY • link 9 months ago Amit • 0

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Untested

ind <- rowSums(abs(Results)) == 3L
lst <- lapply(1:3, function(x) topTable(fit2, x, Inf, sort.by = "n")[ind,])
d.f <- cbind(lst[[1]], do.call(cbind, function(x) lapply(lst[-1], x[,c("logFC","t", "P.Value","adj.P.Val")]))

ADD REPLY • link 9 months ago James W. MacDonald 67k

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Hi James, I have run the script and it gave me only column names and not data.

colnames(d.f) [1] "logFC" "AveExpr" "t" "P.Value" "adj.P.Val" "B" "logFC" "t"
[9] "P.Value" "adj.P.Val" "logFC" "t" "P.Value" "adj.P.Val"

rownames(d.f) character(0)

ADD REPLY • link 9 months ago Amit • 0

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Yes. As I said, untested. When you ran the last line it had to have said

Error in do.call(cbind, function(x) lapply(lst[-1], x[, c("logFC", "t",  : 
  second argument must be a list

Because the last line should actually read

d.f <- cbind(lst[[1]], do.call(cbind, lapply(lst[-1], function(x) x[,c("logFC","t", "P.Value","adj.P.Val")])))

ADD REPLY • link 9 months ago James W. MacDonald 67k

score 2 · Answer 2 · 2024-03-01

This is not a direct answer to your question, but rather a comment and some advice. In most cases you would be better of using the topTable already provided by

topTable(fit2)

rather than trying to hack a new table from the Venn Diagram. This table already provides logFC for all three comparisons together with an overall P-value for differences between the 3 phenotypes.