Showing : de • reset
2
votes
7
replies
2.4k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 4.5 years ago by 51k • written 4.5 years ago by • 0
2
votes
5
replies
3.8k
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 4.6 years ago by ★ 13k • written 4.6 years ago by ▴ 830
5
votes
7
replies
2.6k
views
Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 4.6 years ago by 51k • written 4.6 years ago by ▴ 60
3
votes
5
replies
1.6k
views
Different numbers of DE genes using edgeR and DESEQ2
edger deseq2 rnaseq de
updated 4.6 years ago by 51k • written 4.6 years ago by ▴ 60
6
votes
6
replies
2.4k
views
GO enrichment analysis with goana after performing DE analysis with glmTreat
go DE edger rnaseq glmTreat
updated 4.6 years ago by 51k • written 4.6 years ago by ▴ 60
0
votes
1
reply
1.1k
views
Multi-level experiment with continuous varibles and confounders in limma
limma de differential gene expression multi-tissue design multi-level design
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
3
votes
5
replies
2.5k
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 4.6 years ago by 42k • written 4.6 years ago by ▴ 830
0
votes
3
replies
1.2k
views
DESeq2 - nested samples (individuals) - time course - conditions
deseq2 nested de
updated 5.0 years ago by 42k • written 5.0 years ago by • 0
3
votes
3
replies
1.8k
views
Different number of marker genes between same clusters
sce markers single cell DE clusters
5.2 years ago ludmi.b • 0
2
votes
2
replies
3.0k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq Seurat DE
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
3
votes
4
replies
1.5k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger design matrix de
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 10
1
vote
5
replies
2.0k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 5.7 years ago by 42k • written 5.7 years ago by • 0
7
votes
13
replies
2.2k
views
Taking into account strong batch effect in microarray differential expression analysis with limma
limma microarray hugeneST batch effect DE
updated 5.8 years ago by ★ 7.9k • written 5.8 years ago by ▴ 830
1
vote
1
reply
774
views
different observation of DEG for same group
deseq2 DE
updated 5.8 years ago by 42k • written 5.8 years ago by • 0
0
votes
1
reply
1.1k
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 6.4 years ago by 67k • written 6.4 years ago by • 0
0
votes
5
replies
1.9k
views
DESeq2 for DE analysis in developmental stages of tomato pollen
DESeq2 DE normalization
7.3 years ago mario.keller.1988 ▴ 20
0
votes
2
replies
1.3k
views
coef for limma differential expression analysis
limma DE
updated 7.8 years ago by ▴ 830 • written 7.8 years ago by • 0
0
votes
2
replies
3.7k
views
Using sva ComBat on DESeq2 Data
deseq2 DE rnaseq sva combat
updated 8.8 years ago by 42k • written 8.8 years ago by • 0
1
vote
2
replies
1.9k
views
Error message running DE-test in Monocle
monocle cummerbund DE rnaseq
updated 9.4 years ago by • 0 • written 9.6 years ago by ▴ 260
19 results • Page 1 of 1
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Answer: Downloading Metagenomic Data with Higher Taxonomic Units by Levi Waldron ★ 1.1k
I'm sorry I missed the first post! Yes, it is easy to agglomerate ranks in curatedMetagenomicData datasets. See the example in the vignette…
Comment: Differene between the Wald and LRT test for time-series gene expression data by Denise • 0
This makes a lot of sense, thank you very much!
Comment: Downloading Metagenomic Data with Higher Taxonomic Units by elozanoe • 0
Hi! I'm facing the same problem. Is there any easy way to output relative abundances of higher taxonomic units (up to kingdom), similar to…
Comment: Is it recommended to analyze different tissues together when using edgeR by Gordon Smyth 51k
Just plot the samples with plotMDS(). Alternatively you would use `voomLmFit()` with `sample.weights=TRUE` or `var.group=tissue`. In princ…
Comment: Handling Epic Array Data by Melisa Tecik • 0
Thanks a lot for the help. You saved my day
Votes
A: correcting the batch effects in Limma and SVA
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
Answer: Differene between the Wald and LRT test for time-series gene expression data
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
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