Showing : DE • reset
2
votes
7
replies
1.9k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 3.9 years ago by 50k • written 3.9 years ago by • 0
2
votes
5
replies
3.2k
views
Possible batch effect correction with RNA-Seq data when the batches do not contain both biological conditions for DE analysis
batch effect limma rna seq DE
updated 4.0 years ago by ★ 13k • written 4.0 years ago by ▴ 830
5
votes
7
replies
2.2k
views
Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 60
3
votes
5
replies
1.2k
views
Different numbers of DE genes using edgeR and DESEQ2
edger deseq2 rnaseq de
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 60
6
votes
6
replies
2.0k
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go DE edger rnaseq glmTreat
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 60
0
votes
1
reply
900
views
Multi-level experiment with continuous varibles and confounders in limma
limma de differential gene expression multi-tissue design multi-level design
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
3
votes
5
replies
2.1k
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq rna-seq filtering DE deseq2
updated 4.1 years ago by 41k • written 4.1 years ago by ▴ 830
0
votes
3
replies
978
views
DESeq2 - nested samples (individuals) - time course - conditions
deseq2 nested de
updated 4.4 years ago by 41k • written 4.4 years ago by • 0
3
votes
3
replies
1.4k
views
Different number of marker genes between same clusters
sce markers single cell DE clusters
4.6 years ago ludmi.b • 0
2
votes
2
replies
2.7k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
3
votes
4
replies
1.3k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger design matrix de
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
1
vote
5
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1.7k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
7
votes
13
replies
1.8k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma microarray hugeneST batch effect DE
updated 5.2 years ago by ★ 7.9k • written 5.2 years ago by ▴ 830
1
vote
1
reply
627
views
different observation of DEG for same group
deseq2 DE
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
0
votes
1
reply
944
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
0
votes
5
replies
1.7k
views
DESeq2 for DE analysis in developmental stages of tomato pollen
DESeq2 DE normalization
6.7 years ago mario.keller.1988 ▴ 20
0
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2
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1.2k
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coef for limma differential expression analysis
limma DE
updated 7.2 years ago by ▴ 830 • written 7.2 years ago by • 0
0
votes
2
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3.4k
views
Using sva ComBat on DESeq2 Data
deseq2 DE rnaseq sva combat
updated 8.2 years ago by 41k • written 8.2 years ago by • 0
1
vote
2
replies
1.7k
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Error message running DE-test in Monocle
monocle cummerbund DE rnaseq
updated 8.8 years ago by • 0 • written 9.0 years ago by ▴ 250
19 results • Page 1 of 1
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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