Showing : DEseq2 • reset
1
vote
6
replies
1.6k
views
Validity of using DESeq2 with directly normalized EDASeq counts rather than offset
deseq2 edaseq
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
10
replies
1.2k
views
DESEQ2 1.24 versus 1.14
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
votes
2
replies
1.4k
views
Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 20
0
votes
4
replies
941
views
DESeq2 for repeated/clustered samples
deseq2 repeated measures
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
2
votes
7
replies
2.4k
views
DeSeq2 - Can't fetch any results: Error in .wrap_in_length_one_list_like_object(value, name, x)
deseq2 software error
updated 13 months ago by • 0 • written 6.0 years ago by ▴ 30
3
votes
3
replies
2.1k
views
Issue with scp transfer of DESeq2 objects
deseq2 scp Unix Single-Cell
updated 6.0 years ago by 25k • written 6.0 years ago by ▴ 20
0
votes
9
replies
2.2k
views
DESeq2 with nanostring data
deseq2 nanostring
6.0 years ago acs1990 ▴ 10
0
votes
4
replies
1.7k
views
ddsClean <- ddsTC[which(mcols(ddsTC)$betaConv),] Error in base::which(x, arr.ind, useNames, ...) : argument to 'which' is not logical
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
3
replies
4.2k
views
Normalisation - Deseq2 vs StingTie-Ballgown
deseq2 StringTie RNA-seq normalisation
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
vote
5
replies
4.5k
views
DESeq2 swap ensembl gene id rownames with gene symbol column
deseq2 dataframe ensembl gene id gene symbol entrezid
updated 8 months ago by • 0 • written 6.0 years ago by ▴ 10
0
votes
5
replies
1.2k
views
deseq2 differential gene expression and fold change
deseq2
6.0 years ago Jitendra ▴ 10
1
vote
1
reply
674
views
Analyzing mini-bulk samples with DESeq2
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
1
reply
1.5k
views
Assessing the influence of covariates on RNA-seq in DESeq2
deseq2 rna-sequencing covariates glm
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 20
0
votes
7
replies
1.8k
views
DESEQ2 for circRNA normalisation
DESEQ2 circRNA normalisation
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
2
replies
1.2k
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2 design formula design matrix edgeR ATAC
updated 6.0 years ago by 53k • written 6.0 years ago by • 0
0
votes
1
reply
1.5k
views
DESeq2 - how to run contrasts leaving out one factor, not just using the reference?
deseq2 contrasts reference level
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
4
replies
1.4k
views
>5000 significantly differentially expressed genes
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
2
votes
1
reply
3.5k
views
Understanding interactions in DESeq2
deseq2
updated 6.0 years ago by ★ 1.4k • written 6.0 years ago by • 0
0
votes
2
replies
1.4k
views
DESeq2 changing Rownames (Gene accession numbers)
deseq2
6.0 years ago JGibbons1 • 0
0
votes
1
reply
488
views
DESeq2: downregulation of control sample
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
vote
3
replies
1.5k
views
Collapse Technical Replicates and Group-specific condition effects, individuals nested within groups
deseq2 RNAseq model.matrix collapseTechnicalReplicates
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 50
0
votes
3
replies
598
views
Help with DESeq2 design matrix
deseq2
updated 6.0 years ago by • 0 • written 6.0 years ago by • 0
4
votes
6
replies
3.4k
views
Does DESeq2 Data_transformation (vsd or rld) Change Clustering (and PCA_plot) Results?
DESeq2 rld vsd data transformation ntd
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
1
reply
585
views
Results counts to Deseq object
deseq2 countmatrix
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
3
replies
2.4k
views
Comparing factor levels in deseq2
deseq2
6.0 years ago gv ▴ 40
1
vote
1
reply
1.0k
views
Normalized counts access in DESeq2 R: with and without batch
deseq2 edger normalization
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 60
2
votes
6
replies
1.1k
views
DEseq2 design matrix for paired samples with batch effects
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
3
replies
537
views
DESeq2 DE analysis of two samples conditioned on a shared reference
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
1
reply
1.9k
views
DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 10
0
votes
8
replies
2.5k
views
DESeq2: experiment with two genotypes and three conditions
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
vote
6
replies
1.4k
views
how to correct for age using Deseq2
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
5
votes
2
replies
3.5k
views
How to perform DEseq2 on datasets without replicates or merged replicates
deseq2 R bioconductor RNA_Seq replicates
updated 6.0 years ago by ★ 1.4k • written 6.0 years ago by ▴ 30
0
votes
3
replies
2.3k
views
DESeq2 using 'relevel' for different comparisons
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 60
2
votes
3
replies
976
views
Still lots of NA adjusted p-values in DESeq2 after eliminating Cook's distance cutoff.
deseq2
6.0 years ago ariel ▴ 20
0
votes
1
reply
1.5k
views
DESeq2 very complex design - how extract contrasts of interest?
DESeq2 RNA-Seq Multifactorial Design GLM Contrasts
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
7
replies
851
views
DESeq2: Is it possible to have incomplete pairs of samples?
deseq2
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
2
votes
1
reply
961
views
Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
6.0 years ago Beginner • 0
0
votes
3
replies
793
views
Nested design vs averaging coefficients
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 40
0
votes
2
replies
2.4k
views
WGCNA module Eigengene PC1 and expression correlation
WGCNA DESeq2 RNA-Seq
6.0 years ago Sri Dewi • 0
0
votes
3
replies
1.2k
views
DESeq2 standalone TE usage
deseq2 normalization
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
3
votes
4
replies
1.3k
views
Error when providing contrast coefficients to lfcShrink() of DESeq2 package
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 90
0
votes
2
replies
751
views
Dynamic allocations possible when building DESeq object?
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 30
1
vote
10
replies
11k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 4 months ago by 43k • written 6.0 years ago by • 0
0
votes
2
replies
3.0k
views
How to overcome negative values obtained from vst for downstream analysis ( calculating bray-curtis and PCoA plot)?
zinbwave deseq2 vegan
updated 6.0 years ago by 68k • written 6.0 years ago by • 0
0
votes
5
replies
6.1k
views
DEseq Error in checkForExperimentalReplicates
deseq2
6.0 years ago zhezhenwang • 0
0
votes
4
replies
3.7k
views
Outliers and Filtering with DESEq2 to overcome NA values in padj
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
2
votes
3
replies
1.5k
views
How to correctly set up the design in DESeq2 for RRPP?
deseq2 rrpp DEGs RNAseq
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
6
replies
3.0k
views
CQN to DEseq2
CQN deseq2
updated 3.0 years ago by • 0 • written 6.0 years ago by • 0
0
votes
1
reply
1.5k
views
Is CQN compatible with DESeq2?
deseq2 cqn
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
votes
3
replies
1.5k
views
DESeq2 - nested samples (individuals) - time course - conditions
deseq2 nested de
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
4,839 results • Page 44 of 97
Recent ...
Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to efoss ▴ 10
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Popular Question to story.benjamin ▴ 20
Locations • All
United States, 19 minutes ago
United States, 52 minutes ago
United States, 1 hour ago
Barcelona, Spain, 1 hour ago
United States, 2 hours ago
Traffic: 826 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