Showing : topTable • reset
0
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2
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1.0k
views
decideTests vs topTable results
decideTests topTable limma
updated 16 months ago by 51k • written 16 months ago by ▴ 20
0
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2
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935
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 19 months ago by 51k • written 19 months ago by • 0
0
votes
1
reply
474
views
NAs in some genes in topTable output
limma topTable
updated 21 months ago by 51k • written 21 months ago by ▴ 10
0
votes
2
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1.1k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
3.2 years ago James • 0
2
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4
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2.6k
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 6.2 years ago by • 0
8
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4
replies
1.5k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
3.7 years ago snijesh ▴ 200
0
votes
5
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1.5k
views
eBayes options and decideTests method
limma eBayes decideTests topTable
updated 4.7 years ago by 51k • written 4.7 years ago by • 0
0
votes
3
replies
1.5k
views
Subsetting a data frame generated by topTable() {limma}
limma toptable microarray
updated 5.2 years ago by 51k • written 5.2 years ago by ▴ 30
3
votes
6
replies
2.5k
views
Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix toptable makecontrasts differential gene expression
7.1 years ago stinehedensted • 0
1
vote
1
reply
1.9k
views
limma: The topTable function implementation when outputin the differential expression results from RNA-seq dataset?
limma voom edgeR toptable output
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 10
11
votes
5
replies
14k
views
Limma: how to get same output as topTable but for all the genes ?
limma toptable
updated 7.3 years ago by 51k • written 16.0 years ago by ▴ 190
1
vote
2
replies
1.5k
views
differentially expressed genes without contrasts
limma toptable makecontrasts contrast matrix
updated 7.4 years ago by ★ 7.9k • written 7.4 years ago by • 0
3
votes
3
replies
2.4k
views
Explanation of an ANOVA approach of multiple coefficients in limma with topTable in a microarray analysis
limma ANOVA topTable microarray
updated 8.1 years ago by 51k • written 8.1 years ago by ▴ 80
14
votes
16
replies
3.0k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma toptable
8.4 years ago giroudpaul ▴ 40
8
votes
10
replies
5.3k
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 8.7 years ago by 51k • written 8.7 years ago by ▴ 80
2
votes
2
replies
2.3k
views
Error while calling function topTable() from limma R package in microarray data analysis
limma microarray a4Core topTable statistical inference
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 830
2
votes
4
replies
3.0k
views
Meta-Analysis after running limma on a normalized dataset
meta-analysis limma toptable
updated 9.3 years ago by ★ 28k • written 9.3 years ago by ▴ 20
10
votes
11
replies
8.4k
views
Standard error and effect size from Limma
effect size Limma toptable Standard Error
updated 9.3 years ago by 51k • written 9.3 years ago by ▴ 20
2
votes
4
replies
3.9k
views
report genes in intersection of Venn diagram with topTable?
rnaseq venn diagram limma toptable edgeR
updated 9.4 years ago by 51k • written 9.4 years ago by • 0
6
votes
7
replies
2.4k
views
what causes the difference in the topTable results by the two analyses using limma?
limma topTable
updated 10.1 years ago by ★ 28k • written 10.1 years ago by ▴ 550
20 results • Page 1 of 1
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Replies
Comment: Differential Expression Analysis with unbalanced batches without replication bet by Thili • 0
Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…
Comment: Problem at champ.load by andrew.gibbons • 0
I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…
Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column by GV Yoshikawa • 0
Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Answer: Differential Expression Analysis with unbalanced batches without replication bet by Gordon Smyth 51k
> Is there an alternative model or approach in tools like edgeR, limma-voom, or DESeq2 or any other that can handle confounded batch effect…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected. by Adam • 0
I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…
Votes
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
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