Showing : topTable • reset
14
votes
16
replies
2.7k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma toptable
7.9 years ago giroudpaul ▴ 40
10
votes
11
replies
7.7k
views
Standard error and effect size from Limma
effect size Limma toptable Standard Error
updated 8.8 years ago by 50k • written 8.8 years ago by ▴ 20
8
votes
10
replies
4.9k
views
Interpretation of confidence interval values for logFC returned from topTable function in limma with microarray dataset
limma topTable confidence interval effect size microarray
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 80
6
votes
7
replies
2.2k
views
what causes the difference in the topTable results by the two analyses using limma?
limma topTable
updated 9.6 years ago by ★ 28k • written 9.6 years ago by ▴ 550
3
votes
6
replies
2.2k
views
Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix toptable makecontrasts differential gene expression
6.6 years ago stinehedensted • 0
11
votes
5
replies
13k
views
Limma: how to get same output as topTable but for all the genes ?
limma toptable
updated 6.8 years ago by 50k • written 15.4 years ago by ▴ 190
0
votes
5
replies
1.2k
views
eBayes options and decideTests method
limma eBayes decideTests topTable
updated 4.2 years ago by 50k • written 4.2 years ago by • 0
2
votes
4
replies
2.8k
views
Meta-Analysis after running limma on a normalized dataset
meta-analysis limma toptable
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 20
6
votes
4
replies
1.2k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
3.2 years ago snijesh ▴ 20
2
votes
4
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3.7k
views
report genes in intersection of Venn diagram with topTable?
rnaseq venn diagram limma toptable edgeR
updated 8.9 years ago by 50k • written 8.9 years ago by • 0
2
votes
4
replies
2.3k
views
Why my limma DEG result in top Table all without significant meaning,showing logFC <1.5 or logFC>-1.5 ?
limma toptable deg logfc
written 5.7 years ago by • 0
3
votes
3
replies
2.1k
views
Explanation of an ANOVA approach of multiple coefficients in limma with topTable in a microarray analysis
limma ANOVA topTable microarray
updated 7.6 years ago by 50k • written 7.6 years ago by ▴ 80
0
votes
3
replies
1.4k
views
Subsetting a data frame generated by topTable() {limma}
limma toptable microarray
updated 4.6 years ago by 50k • written 4.6 years ago by ▴ 30
0
votes
2
replies
688
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 13 months ago by 50k • written 13 months ago by • 0
2
votes
2
replies
2.1k
views
Error while calling function topTable() from limma R package in microarray data analysis
limma microarray a4Core topTable statistical inference
updated 8.3 years ago by ★ 28k • written 8.3 years ago by ▴ 830
1
vote
2
replies
1.3k
views
differentially expressed genes without contrasts
limma toptable makecontrasts contrast matrix
updated 6.8 years ago by ★ 7.9k • written 6.8 years ago by • 0
0
votes
2
replies
970
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
2.7 years ago James • 0
0
votes
2
replies
749
views
decideTests vs topTable results
decideTests topTable limma
updated 10 months ago by 50k • written 10 months ago by ▴ 20
1
vote
1
reply
1.7k
views
limma: The topTable function implementation when outputin the differential expression results from RNA-seq dataset?
limma voom edgeR toptable output
updated 6.8 years ago by ★ 28k • written 6.8 years ago by ▴ 10
0
votes
1
reply
361
views
NAs in some genes in topTable output
limma topTable
updated 15 months ago by 50k • written 15 months ago by ▴ 10
20 results • Page 1 of 1
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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