Showing : DeSeq2 • reset
2
votes
2
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778
views
With DESeq2 "Not full rank" Error with design
DESeq2 DEs
20 months ago feather-W • 0
0
votes
2
replies
1.2k
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 20 months ago by 43k • written 20 months ago by • 0
0
votes
4
replies
881
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 20 months ago by 43k • written 20 months ago by • 0
0
votes
10
replies
1.7k
views
DESeq2 filtering vs edgeR filtering
DESeq2
written 20 months ago by • 0
0
votes
2
replies
3.1k
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
20 months ago kcarey • 0
1
vote
1
reply
593
views
i'm not getting any differentially expressed genes.
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
2
votes
1
reply
815
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2 tximport
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
1
vote
1
reply
522
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
1
vote
3
replies
1.0k
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 22 months ago by • 0
0
votes
2
replies
954
views
DESeq2: Comparing A Knockout to a Strain
DESeq2
21 months ago Viktor Thiel • 0
0
votes
1
reply
845
views
DESeq2 for pseudobulk analysis of scCITE-seq
DESeq2 scCITE-seq
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
votes
8
replies
1.5k
views
DESeq and SVA for batch effect
DESeq2 BatchEffect sva
21 months ago michelafrancesconi8 • 0
0
votes
1
reply
667
views
Unusually large fold-changes in Deseq2 results
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
1
vote
4
replies
917
views
DESeq2 Replicates
DESeq2 RNASeq
21 months ago kcarey • 0
2
votes
6
replies
1.0k
views
Factor vs Character in design
DESeq2
21 months ago James Aiden • 0
1
vote
3
replies
1.0k
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2 glmGamPoi
21 months ago I-Hsuan Lin ▴ 10
4
votes
7
replies
1.9k
views
weird volcano plot
DESeq2
updated 21 months ago by • 0 • written 2.1 years ago by ▴ 10
0
votes
1
reply
733
views
DEseq2 dispersion plot
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
1
vote
3
replies
1.1k
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 21 months ago by ★ 1.4k • written 21 months ago by ▴ 10
0
votes
2
replies
1.1k
views
Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
votes
3
replies
947
views
Would I treat surrogate variables as batches?
DESeq2 sva
updated 21 months ago by 68k • written 21 months ago by ▴ 10
0
votes
1
reply
700
views
Changed DESeq2 comparison value but the heatmap is still the same
DESeq2 pheatmap
updated 21 months ago by 68k • written 21 months ago by • 0
1
vote
4
replies
999
views
Further clarification of unbalanced group sizes DESeq2
DESeq2
21 months ago hmillike • 0
0
votes
1
reply
478
views
few significant genes from DESeq2 analysis
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
1
vote
4
replies
1.5k
views
DEseq2 coefficient
DESeq2 coefficient
21 months ago • updated 19 months ago JKim • 0
3
votes
5
replies
1.8k
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
2
votes
1
reply
747
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 21 months ago by 43k • written 21 months ago by ▴ 10
2
votes
2
replies
831
views
locfunc not found in DESeq2
locfunc DESeq2 shorth estimateSizeFactors
21 months ago Hope ▴ 10
1
vote
2
replies
854
views
evaluate the variable importance on genes
DESeq2 deseq
21 months ago Meme • 0
0
votes
3
replies
833
views
library sizes differ extremely after dds
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
1
vote
4
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1.5k
views
Comparing gene expression across three tissue types to identify any difference.
DESeq2
21 months ago James Aiden • 0
0
votes
13
replies
1.9k
views
Unexpected behavior of lfcShrink() function in DESeq2 analysis
DESeq2 SmallRNA
updated 21 months ago by 43k • written 21 months ago by • 0
1
vote
5
replies
985
views
vst transformation and zero counts
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by ▴ 740
1
vote
12
replies
2.7k
views
How to calculate p value when comparing two sets of DEGs and not applying interaction
DEGcomparison DESeq2 InteractionSet pvalue
21 months ago paria.alipour • 0
0
votes
3
replies
1.4k
views
utf-8 codec can't decode byte 0xd5
importr DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
1
reply
488
views
Problems with filtering DESeq Results (log2fold change)
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
votes
3
replies
1.2k
views
DESeq2: Adjust for treatment effect patient vs control
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
1
reply
1.9k
views
Pseudobulk-DESeq2 analyze multiple cell types at once?
pseudobulk DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
7
replies
1.3k
views
DESeq filtering specific to contrasts
DESeq2
updated 19 months ago by 43k • written 21 months ago by • 0
0
votes
2
replies
851
views
help checking the design matrix and contrast in DESeq2 "not full rank" scenario
DESeq2
21 months ago ccshao ▴ 70
0
votes
1
reply
667
views
Double batch effect (Individuals nested within blocks in DESeq2)
DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
1
vote
2
replies
962
views
DESeq2 issue: can't create DESeq2 object
DESeq2 RBioinf
21 months ago Magdalena • 0
0
votes
1
reply
457
views
Inconsistency in DESeq2 Log fold change
DESeq2
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
votes
3
replies
766
views
DESeq2 Results in Different Pvalue & Log2FC using the same code and data
DESeq2 dese
written 21 months ago by • 0
0
votes
5
replies
1.2k
views
DESEQ2 Repeated Measures-like design error help
DESeq2
updated 21 months ago by 43k • written 22 months ago by ▴ 10
0
votes
3
replies
1.1k
views
DESeq2 interaction terms RIPseq analysis
DESeq2 RIPSeq
updated 22 months ago by 43k • written 22 months ago by • 0
2
votes
2
replies
1.7k
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
22 months ago jackafiore • 0
4
votes
2
replies
2.7k
views
How to do DESeq2 on Kallisto Data
DESeq2 Kallisto
updated 22 months ago by ▴ 40 • written 22 months ago by • 0
1
vote
2
replies
2.4k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.6 years ago by • 0
0
votes
2
replies
731
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
22 months ago Lily Cheang ▴ 10
4,840 results • Page 7 of 97
Recent ...
Replies
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: 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
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
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Popular Question to James W. MacDonald 68k
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