Showing : topTable • reset
0
votes
2
replies
1.4k
views
decideTests vs topTable results
decideTests topTable limma
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 20
0
votes
2
replies
1.2k
views
Full list of differential genes not obtained in topTable
Microarray GEOquery topTable limma
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
votes
1
reply
673
views
NAs in some genes in topTable output
limma topTable
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 10
0
votes
2
replies
1.4k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
4.2 years ago James • 0
2
votes
4
replies
3.0k
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 7.1 years ago by • 0
9
votes
4
replies
1.9k
views
Limma outputs different results for same sample?
topTable MicroarrayData ebayes limma Microarray
4.7 years ago snijesh ▴ 200
0
votes
5
replies
1.9k
views
eBayes options and decideTests method
limma eBayes decideTests topTable
updated 5.7 years ago by 53k • written 5.7 years ago by • 0
0
votes
3
replies
1.8k
views
Subsetting a data frame generated by topTable() {limma}
limma toptable microarray
updated 6.1 years ago by 53k • written 6.1 years ago by ▴ 30
3
votes
6
replies
2.9k
views
Help to understand my contrast.matrix and to interpret my topTable results
contrast matrix toptable makecontrasts differential gene expression
8.1 years ago stinehedensted • 0
1
vote
1
reply
2.3k
views
limma: The topTable function implementation when outputin the differential expression results from RNA-seq dataset?
limma voom edgeR toptable output
updated 8.2 years ago by ★ 29k • written 8.2 years ago by ▴ 10
12
votes
5
replies
15k
views
Limma: how to get same output as topTable but for all the genes ?
limma toptable
updated 8.3 years ago by 53k • written 16.9 years ago by ▴ 190
1
vote
2
replies
1.7k
views
differentially expressed genes without contrasts
limma toptable makecontrasts contrast matrix
updated 8.3 years ago by ★ 7.9k • written 8.3 years ago by • 0
3
votes
3
replies
2.7k
views
Explanation of an ANOVA approach of multiple coefficients in limma with topTable in a microarray analysis
limma ANOVA topTable microarray
updated 9.1 years ago by 53k • written 9.1 years ago by ▴ 90
14
votes
16
replies
3.7k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma toptable
9.4 years ago giroudpaul ▴ 40
8
votes
10
replies
6.0k
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 9.6 years ago by 53k • written 9.6 years ago by ▴ 90
2
votes
2
replies
2.7k
views
Error while calling function topTable() from limma R package in microarray data analysis
limma microarray a4Core topTable statistical inference
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 840
2
votes
4
replies
3.4k
views
Meta-Analysis after running limma on a normalized dataset
meta-analysis limma toptable
updated 10.3 years ago by ★ 29k • written 10.3 years ago by ▴ 20
10
votes
11
replies
9.6k
views
Standard error and effect size from Limma
effect size Limma toptable Standard Error
updated 10.3 years ago by 53k • written 10.3 years ago by ▴ 20
2
votes
4
replies
4.1k
views
report genes in intersection of Venn diagram with topTable?
rnaseq venn diagram limma toptable edgeR
updated 10.4 years ago by 53k • written 10.4 years ago by • 0
6
votes
7
replies
2.8k
views
what causes the difference in the topTable results by the two analyses using limma?
limma topTable
updated 11.1 years ago by ★ 29k • written 11.1 years ago by ▴ 550
20 results • Page 1 of 1
Recent ...
Replies
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
Awards • All
Popular Question to Ou, Jianhong ★ 1.3k
Popular Question to Maria Doyle ▴ 100
Popular Question to Gordon Smyth 53k
Oracle to shepherl 4.2k
Popular Question to Matej • 0
Locations • All
The city by the bay, 2 minutes ago
United States, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
France, 2 hours ago
Pittsburgh, United States, 2 hours ago
Traffic: 1551 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6