Showing : toptable • reset
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
10
votes
11
replies
7.6k
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
4.8k
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 8.1 years ago by 50k • written 8.1 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
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 5.6 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
2.0k
views
Error while calling function topTable() from limma R package in microarray data analysis
limma microarray a4Core topTable statistical inference
updated 8.2 years ago by ★ 28k • written 8.2 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 6.7 years ago by ★ 28k • written 6.7 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
961
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
735
views
decideTests vs topTable results
decideTests topTable limma
updated 10 months ago by 50k • written 10 months ago by ▴ 20
0
votes
2
replies
677
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
356
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: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
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Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
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For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
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Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
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Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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