Showing : topTable • reset
11
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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 15.5 years ago by ▴ 190
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
2
votes
4
replies
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
2.8k
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
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
2
votes
4
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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
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
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
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
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
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
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
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
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
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
0
votes
2
replies
971
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
755
views
decideTests vs topTable results
decideTests topTable limma
updated 10 months ago by 50k • written 10 months ago by ▴ 20
0
votes
2
replies
693
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
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
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Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data by Robert Castelo ★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Comment: deseq2 results by ATpoint ★ 4.1k
> the results are not satisfactory to me Well, what is your question? The DESeq2 vignette covers how to do analysis, and some diagnostics…
Comment: Extremely small p-values using Limma for proteomic data by ATpoint ★ 4.1k
It's not an implementation problem I am discussing (it's trivial obviously) -- more that for most purposes the y-axis metric should be the …
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
Answer: Cannot connect to ExperimentHub server
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