Showing : de • reset
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 5.3 years ago by ★ 7.9k • written 5.3 years ago by ▴ 830
2
votes
7
replies
2.0k
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
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
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
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
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
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
1
vote
5
replies
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
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
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
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
0
votes
3
replies
983
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
1
vote
2
replies
1.7k
views
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
0
votes
2
replies
1.2k
views
coef for limma differential expression analysis
limma DE
updated 7.2 years ago by ▴ 830 • written 7.2 years ago by • 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
0
votes
2
replies
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
1
reply
629
views
different observation of DEG for same group
deseq2 DE
updated 5.3 years ago by 41k • written 5.3 years ago by • 0
0
votes
1
reply
945
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
1
reply
908
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
19 results • Page 1 of 1
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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