Showing : DESEq2 • reset
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DESeq2 Design - Within & Between Specimen Comparisons
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 20
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6
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1.6k
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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
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10
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1.2k
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DESEQ2 1.24 versus 1.14
deseq2
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
0
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2
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1.4k
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Coefficient names for multiple group comparisons to use with lfcShrink & apeglm
deseq2 lfcShrink apeglm
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 20
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4
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942
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DESeq2 for repeated/clustered samples
deseq2 repeated measures
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
2
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7
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2.4k
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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
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3
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2.1k
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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
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9
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2.2k
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DESeq2 with nanostring data
deseq2 nanostring
6.0 years ago acs1990 ▴ 10
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4
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1.7k
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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
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3
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4.2k
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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
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5
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4.5k
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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
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5
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1.2k
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deseq2 differential gene expression and fold change
deseq2
6.0 years ago Jitendra ▴ 10
1
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1
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674
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Analyzing mini-bulk samples with DESeq2
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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1
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1.5k
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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
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7
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1.8k
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DESEQ2 for circRNA normalisation
DESEQ2 circRNA normalisation
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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2
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1.2k
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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
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1
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1.5k
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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
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4
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1.4k
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>5000 significantly differentially expressed genes
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
2
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1
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3.5k
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Understanding interactions in DESeq2
deseq2
updated 6.0 years ago by ★ 1.4k • written 6.0 years ago by • 0
0
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2
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1.4k
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DESeq2 changing Rownames (Gene accession numbers)
deseq2
6.0 years ago JGibbons1 • 0
0
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1
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489
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DESeq2: downregulation of control sample
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
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3
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1.5k
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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
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3
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600
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Help with DESeq2 design matrix
deseq2
updated 6.0 years ago by • 0 • written 6.0 years ago by • 0
4
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6
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3.4k
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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
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1
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585
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Results counts to Deseq object
deseq2 countmatrix
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
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3
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2.4k
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Comparing factor levels in deseq2
deseq2
6.0 years ago gv ▴ 40
1
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1
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1.0k
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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
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6
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1.1k
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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
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3
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537
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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
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1
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1.9k
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DESeq2 counts function not working
deseq2 Deseq RNAseq
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 10
0
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8
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2.5k
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DESeq2: experiment with two genotypes and three conditions
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
1
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6
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1.4k
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how to correct for age using Deseq2
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
5
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2
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3.5k
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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
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3
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2.3k
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DESeq2 using 'relevel' for different comparisons
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 60
2
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3
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976
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Still lots of NA adjusted p-values in DESeq2 after eliminating Cook's distance cutoff.
deseq2
6.0 years ago ariel ▴ 20
0
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1
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1.5k
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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
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7
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851
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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
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1
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961
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Detecting the power in differential expression
POWER DESEQ2 edger LIMMA DIfferential expression
6.0 years ago Beginner • 0
0
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3
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793
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Nested design vs averaging coefficients
deseq2
updated 6.0 years ago by 43k • written 6.0 years ago by ▴ 40
0
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2
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2.4k
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WGCNA module Eigengene PC1 and expression correlation
WGCNA DESeq2 RNA-Seq
6.0 years ago Sri Dewi • 0
0
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3
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1.2k
views
DESeq2 standalone TE usage
deseq2 normalization
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
3
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4
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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
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2
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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
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10
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11k
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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
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2
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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
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5
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6.1k
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DEseq Error in checkForExperimentalReplicates
deseq2
6.0 years ago zhezhenwang • 0
0
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4
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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
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3
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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
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6
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3.0k
views
CQN to DEseq2
CQN deseq2
updated 3.0 years ago by • 0 • written 6.0 years ago by • 0
0
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1
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1.5k
views
Is CQN compatible with DESeq2?
deseq2 cqn
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
4,840 results • Page 44 of 97
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Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
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.
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
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Popular Question to shepherl 4.2k
Popular Question to Gordon Smyth 53k
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Popular Question to James W. MacDonald 68k
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