Showing : toptable • reset
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Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 8 weeks ago by 47k • written 8 weeks ago by • 0
0
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1
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161
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NAs in some genes in topTable output
limma topTable
updated 4 months ago by 47k • written 4 months ago by ▴ 10
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2
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640
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limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
21 months ago James • 0
2
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4
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1.9k
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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 4.7 years ago by • 0
6
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4
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873
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Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
2.3 years ago snijesh ▴ 20
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5
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744
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eBayes options and decideTests method
limma eBayes decideTests topTable
updated 3.3 years ago by 47k • written 3.3 years ago by • 0
0
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3
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989
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Subsetting a data frame generated by topTable() {limma}
limma toptable microarray
updated 3.7 years ago by 47k • written 3.7 years ago by ▴ 30
3
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6
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1.7k
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Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix toptable makecontrasts differential gene expression
5.7 years ago stinehedensted • 0
0
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1
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1.3k
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limma: The topTable function implementation when outputin the differential expression results from RNA-seq dataset?
limma voom edgeR toptable output
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 10
11
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5
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12k
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Limma: how to get same output as topTable but for all the genes ?
limma toptable
updated 5.8 years ago by 47k • written 14.5 years ago by ▴ 190
1
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2
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993
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differentially expressed genes without contrasts
limma toptable makecontrasts contrast matrix
updated 5.9 years ago by 7.8k • written 5.9 years ago by • 0
3
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3
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1.7k
views
Explanation of an ANOVA approach of multiple coefficients in limma with topTable in a microarray analysis
limma ANOVA topTable microarray
updated 6.7 years ago by 47k • written 6.7 years ago by ▴ 80
14
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16
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2.0k
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TopTable Problem : Unique Adj.P.Val which is near 1
limma toptable
7.0 years ago giroudpaul ▴ 40
8
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10
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4.1k
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 7.2 years ago by 47k • written 7.2 years ago by ▴ 80
2
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2
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1.6k
views
Error while calling function topTable() from limma R package in microarray data analysis
limma microarray a4Core topTable statistical inference
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 810
2
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4
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2.4k
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Meta-Analysis after running limma on a normalized dataset
meta-analysis limma toptable
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 20
10
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11
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6.3k
views
Standard error and effect size from Limma
effect size Limma toptable Standard Error
updated 7.9 years ago by 47k • written 7.9 years ago by ▴ 20
2
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4
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3.4k
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report genes in intersection of Venn diagram with topTable?
rnaseq venn diagram limma toptable edgeR
updated 7.9 years ago by 47k • written 7.9 years ago by • 0
6
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7
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1.7k
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what causes the difference in the topTable results by the two analyses using limma?
limma topTable
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 550
19 results • Page 1 of 1
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Replies
Comment: Visualization of negative log CPM values by Gordon Smyth 47k
Sorry, but some of the things you say are not correct. > compound B has 2 statistically significant genes that are up-regulated No, there…
Comment: Visualization of negative log CPM values by ATpoint ★ 2.8k
Applies to both.
Comment: Visualization of negative log CPM values by Sabiha ▴ 10
@atpoint OK, are you referring to the `log2(cpm+1)` or `log2(tpm+1)`
Comment: Visualization of negative log CPM values by Sabiha ▴ 10
@gordonsmyth noted. Related to the graphs above, the table below is the output from `limma`, and compound B has 2 statistically significant…
Comment: Visualization of negative log CPM values by Gordon Smyth 47k
> negative scale might perhaps indicate gene is too low to be really expressed. Yes, negative logCPMs do mean that the gene is expressed a…
Votes
Comment: Visualization of negative log CPM values
Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?
Filtering low intensity probes in microarray data
Comment: Visualization of negative log CPM values
Adjusting for baseline when having longitudinal data, mixed model and no treatment
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