Showing : DESEq2 • reset
3
votes
3
replies
1.2k
views
DESeq2 reports high logFC but not in matrix
deseq2
5.3 years ago Raj • 0
3
votes
4
replies
4.4k
views
Deseq2's geometric mean calculation and 0s
deseq2 normalization
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
0
votes
2
replies
843
views
Custom dispersion estimate DESeq2
deseq2 edger
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ▴ 110
3
votes
7
replies
7.2k
views
limma::removeBatchEffect into DESeq2
deseq2 limma batch effect
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
1
vote
4
replies
2.5k
views
Issues with DESeq2 LRT for time-course experiment
rna-seq R DESeq2 LRT
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 10
2
votes
5
replies
1.9k
views
stat value is throwed out after lfcShrink in DESeq2
deseq2
updated 15 months ago by 43k • written 5.3 years ago by ▴ 40
18
votes
4
replies
43k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2 metagenomics
updated 5.3 years ago by ▴ 220 • written 5.3 years ago by ▴ 10
2
votes
7
replies
2.1k
views
can the counts extracted from Diffbind be used to analysis in Deseq2 as the RNAseq?
deseq2 diffbind
updated 3.6 years ago by ★ 5.2k • written 5.3 years ago by ▴ 10
8
votes
16
replies
6.9k
views
Transcript-level differential expression using DESeq2
deseq2 transcript-level differential expression
updated 3.5 years ago by • 0 • written 5.3 years ago by ▴ 20
17
votes
13
replies
22k
views
deseq2 normalized data with heatmap
deseq2
updated 4.4 years ago by ▴ 10 • written 5.3 years ago by ▴ 20
0
votes
5
replies
1.2k
views
DESeq2 reporting >10,000 DEGs
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
5
votes
4
replies
2.5k
views
how to understand DESeq2 results comparison
deseq2
updated 5.3 years ago by ★ 1.4k • written 5.3 years ago by ▴ 20
4
votes
5
replies
4.2k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
2
votes
8
replies
6.0k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
5.3 years ago Pietro ▴ 40
2
votes
5
replies
1.6k
views
the results from normalized=TRUE and normalized = FALSE is the same
R deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
0
votes
5
replies
1.2k
views
Testing effect of multiple continuous variables using DESeq2
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
3
replies
1.1k
views
Error using DESeq2's nbinomLRT
deseq2 LRT
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 30
6
votes
4
replies
4.0k
views
Having TMM for GSEA
edger deseq2
updated 4.7 years ago by ★ 4.0k • written 5.3 years ago by ▴ 30
0
votes
2
replies
819
views
Problems regarding DESeq2 package installation in R
deseq2
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
1
vote
2
replies
766
views
Unexpected rlog values when count spread is large
deseq2 normalization
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
1
reply
1.1k
views
Differential expression analysis comparison using more that two variables
deseq2 Tutorial
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by • 0
2
votes
8
replies
2.8k
views
Differential gene expression using R
deseq2 edger normalization limma
updated 5.3 years ago by 53k • written 5.3 years ago by • 0
1
vote
4
replies
2.5k
views
Using different LFC shrinkage estimators for spike-in normalised RNA-seq data
deseq2 apeglm rna-seq spike-in
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
0
votes
1
reply
1.1k
views
How to describe LRT test condition for time series RNA-seq data of 2 varieties
deseq2 LRT RNAseq condition
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 30
3
votes
2
replies
2.9k
views
lfcShrink function in DEseq2 and s-values
deseq2 apeglm
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
3
votes
3
replies
1.1k
views
droplevels not working - error in DESeq() function
deseq2
5.3 years ago DcL-A • 0
1
vote
3
replies
871
views
Normalizing counts for cross-species correlation test
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
3
votes
2
replies
1.8k
views
Variance stabilized values and batch correction
deseq2 vst
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
0
votes
1
reply
481
views
DESeq2 differentially expressed genes
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
7
votes
8
replies
2.9k
views
Cook's Distance Outliers: None reported in results table and "cooksCutoff" modification has no effect
deseq2 outliers cooks cooks distance
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
1
reply
1.0k
views
Can I add raw counts for duplicated genes?
DESeq2 RNAseq
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
12
replies
3.1k
views
Error Message in DESEQ (DESEQDataSetFromMatrix)
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
2
votes
2
replies
1.7k
views
Time series RNA-Seq data analysis using DESEQ2
deseq2
updated 5.3 years ago by ★ 4.0k • written 5.3 years ago by ▴ 10
0
votes
1
reply
734
views
Missing Point in PCA Analysis
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
votes
2
replies
1.5k
views
RSEM for DESeq2 without abundance matrix
tximport deseq2 rsem
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
0
votes
1
reply
693
views
Obtaining expanded model matrices when using apeglm
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
0
votes
10
replies
1.5k
views
Deseq2 nested LRT analysis
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
1
vote
2
replies
9.0k
views
DESeq2 normalization and TPM
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 100
0
votes
1
reply
406
views
Normalising allele-specific reads from RNA seq
deseq2
5.3 years ago chandel12oct • 0
8
votes
5
replies
8.5k
views
Understanding interaction term in DESeq2
deseq2 design formula log fold change
updated 15 months ago by 43k • written 5.3 years ago by ▴ 40
1
vote
1
reply
1.2k
views
Error in importing Salmon quantification to R using tximeta
deseq2 tximeta
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
1
vote
1
reply
961
views
Error in importing Salmon quantifications into R with tximport
deseq2 tximport
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 10
3
votes
7
replies
1.8k
views
DESeq2 Interspecies comparisons
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
0
votes
1
reply
534
views
Paired samples in design including 2 conditions and 4 drug dosages
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
votes
3
replies
1.5k
views
Differential gene expression using DESeq2 on Ribo-Seq data
DESeq2 Ribo-Seq differential gene expression
5.3 years ago DataFanatic ▴ 10
0
votes
1
reply
1.7k
views
Can I use pseudocounts for differential abundance of OTUs?
metagenomics deseq2 PHYLOSEQ
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
2
votes
1
reply
2.0k
views
tximport samples.txt file mandatory vs. optional colnames?
tximport salmon deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
0
votes
3
replies
1.7k
views
dealing with BATCH effect/ donor variation in RNA seq data
deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
1
vote
9
replies
4.7k
views
DESeq: Error in model.matrix.formula(design(object), data = colData(object)) : data must be a data.frame
deseq2
updated 5.3 years ago by ▴ 10 • written 9.7 years ago by ▴ 10
1
vote
6
replies
1.6k
views
DESeq2 size factors change with fixed geometric means
size factors deseq2
updated 5.3 years ago by 43k • written 5.3 years ago by • 0
4,840 results • Page 37 of 97
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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.
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.
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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