Showing : de • reset
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
2
votes
5
replies
3.3k
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 4.1 years ago by ★ 13k • written 4.1 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 4.1 years ago by 50k • written 4.1 years ago by ▴ 60
3
votes
5
replies
1.3k
views
Different numbers of DE genes using edgeR and DESEQ2
edger deseq2 rnaseq de
updated 4.1 years ago by 50k • written 4.1 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 4.1 years ago by 50k • written 4.1 years ago by ▴ 60
0
votes
1
reply
924
views
Multi-level experiment with continuous varibles and confounders in limma
limma de differential gene expression multi-tissue design multi-level design
updated 4.1 years ago by ★ 28k • written 4.1 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 42k • written 4.1 years ago by ▴ 830
0
votes
3
replies
1.0k
views
DESeq2 - nested samples (individuals) - time course - conditions
deseq2 nested de
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
3
votes
3
replies
1.5k
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 4.7 years ago by ★ 28k • written 4.7 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 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 10
1
vote
5
replies
1.7k
views
Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
deseq2 DE DEG
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
7
votes
13
replies
1.9k
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
1
vote
1
reply
652
views
different observation of DEG for same group
deseq2 DE
updated 5.3 years ago by 42k • written 5.3 years ago by • 0
0
votes
1
reply
957
views
Interactions and contrasts for DE analysis in ballgown
ballgown R RNAseq DE interactions
updated 5.9 years ago by 65k • written 5.9 years ago by • 0
0
votes
5
replies
1.7k
views
DESeq2 for DE analysis in developmental stages of tomato pollen
DESeq2 DE normalization
6.8 years ago mario.keller.1988 ▴ 20
0
votes
2
replies
1.2k
views
coef for limma differential expression analysis
limma DE
updated 7.3 years ago by ▴ 830 • written 7.3 years ago by • 0
0
votes
2
replies
3.4k
views
Using sva ComBat on DESeq2 Data
deseq2 DE rnaseq sva combat
updated 8.3 years ago by 42k • written 8.3 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 9.1 years ago by ▴ 250
19 results • Page 1 of 1
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Replies
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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