Showing : DESEq2 • reset
2
votes
3
replies
3.0k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
0
votes
1
reply
999
views
DESeq2 interaction design
DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
1
reply
2.8k
views
DESeq2 error after installing BiocManager
scRNAseq RStudio DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
3
votes
4
replies
2.0k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
2.3 years ago Eva ▴ 10
2
votes
4
replies
1.4k
views
DESeq2 "Not full rank" and "Less than full rank" Errors with design ~ time + ind.nested + time:ind.nested
DESeq2
2.3 years ago Erika • 0
0
votes
1
reply
806
views
Model matrix not full rank
DESeq2
2.3 years ago isabelle.dupanloup • 0
1
vote
2
replies
824
views
Differential expression analysis with 7 factors (levels) at once?
DESeq2
2.3 years ago melander • 0
2
votes
2
replies
857
views
DESeq2: full model matrix is less than full rank
DESeq2
2.3 years ago melander • 0
0
votes
3
replies
4.1k
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by ▴ 10
0
votes
4
replies
1.4k
views
DESeq2 & RUVseq model matrix is less than full rank
RUVSeq DESeq2
2.3 years ago anne.hoffrichter • 0
0
votes
4
replies
1.1k
views
Multi factor design and removing the effect of sex on main factor
DESeq2
2.3 years ago Mahendra • 0
0
votes
2
replies
3.1k
views
DESeq2 discrepancy in log2FC significance and normalized counts significance
RNASeqData DESeq2
2.3 years ago Marina • 0
1
vote
3
replies
1.2k
views
DESeq differential expression results are too stringet. How to relax my criteria
shrinkage DifferentialExpression DESeq2
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by ▴ 10
0
votes
6
replies
2.0k
views
Same few genes repeated in DESeq2 Results
DESeq2
2.3 years ago dsambo ▴ 10
0
votes
5
replies
1.4k
views
DESeq2 analysis
DESe DESeq2
2.3 years ago Adèle • 0
4
votes
9
replies
3.7k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
2.3 years ago Luca • 0
0
votes
1
reply
704
views
Using DEseq2 for two conditions with different dispersions
DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
0
replies
829
views
Can't get working R 3.6.3 and 4.2.3 with DESEq2 if compiled by AMD CLANG at Ubuntu 22.04 x64
CLANG DESeq2
2.4 years ago lokapal • 0
1
vote
2
replies
905
views
I changed the reference in DGE contrasts by DESeq2, but the results changed just a bit and not in the sign of Log2FC (positive to negative and invers…
RNASeqData DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
0
votes
8
replies
1.4k
views
Deseq2 Results are different using batch design
DESeq2
2.4 years ago hemantcnaik • 0
1
vote
2
replies
827
views
Building Multifactor Model in DESeq2
DESeq2
2.4 years ago Abhishek Singh ▴ 20
0
votes
11
replies
3.1k
views
Unable to install DESeq2
DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
votes
2
replies
1.3k
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
2.4 years ago Matteo • 0
0
votes
2
replies
1.8k
views
Creating heatmaps with 2 Log Fold Changes in DESEQ2
DESeq2
written 2.4 years ago by • 0
0
votes
1
reply
609
views
Tximport - Is transcript level expression sum equal to summarisetogene() results
tximpor DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
1
vote
2
replies
917
views
DGE analysis for diseased samples through DESeq2 and Ballgown
DESeq2 DGEanalysis ballgown Ballgown DiseasedvsNormal
2.4 years ago Bushra • 0
0
votes
4
replies
1.4k
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2 apeglm DESeq ApeGLM Ashr
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Specifying design in DESeqDataSetFromMatrix
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
1
vote
1
reply
1.6k
views
DESeq2 LRT Reduced Formula
DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
votes
2
replies
558
views
Complex DESeq2 Experimental Design
DESEq2 DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
1
vote
9
replies
1.5k
views
DESeq2 not replicable results
RNASeqData DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
0
votes
3
replies
914
views
p-value<0.05 for a gene with zero counts?
DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
2
votes
1
reply
724
views
Running DEseq2 without "factor" gives unexpected results
DESeq2
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
2
votes
1
reply
1.3k
views
DESeq2 time course using fitted splines
RNASeqData TimeCourse DESeq2 timecoursedata
updated 17 months ago by 43k • written 2.4 years ago by • 0
4
votes
5
replies
3.8k
views
DESeq2, time-course interpretation
Transcriptomics TimeCourse DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by • 0
7
votes
3
replies
1.7k
views
Proper way to implement DESeq2 when comparing samples with trisomies?
DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
0
votes
3
replies
1.6k
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
votes
1
reply
964
views
Controlling for covariates and identifying DEGs using DESeq2
RNASeqData DESeq2
updated 2.4 years ago by 43k • written 2.4 years ago by ▴ 20
8
votes
7
replies
3.1k
views
Scaling DEXSeq estimateDispersions for large datasets, glmGamPoi?
DESeq2 glmGamPoi DEXSeq
updated 2.4 years ago by ▴ 20 • written 3.1 years ago by ▴ 20
1
vote
8
replies
2.6k
views
DESeq2 test for synergistic vs additive effects
synergistic additive DESeq2
updated 20 months ago by ★ 13k • written 2.4 years ago by ▴ 10
2
votes
9
replies
2.4k
views
Importing RSEM processed data already formatted as a summarized experiment into DESeq2
tximport tximportData DESeq2
2.4 years ago Ndimensional ▴ 20
2
votes
3
replies
1.9k
views
Identify highly variable genes after vst
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
5
replies
1.9k
views
DESeq2 design formula
designformula DESeq2
updated 2.4 years ago by ★ 1.4k • written 2.4 years ago by • 0
0
votes
1
reply
1.2k
views
really low padj value from DESeq2
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
1
vote
1
reply
1.0k
views
DESEQ2 differential expression for subsets of data?
RNASeqData DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 10
0
votes
2
replies
913
views
plotCounts label each sample
p DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
2
replies
1.3k
views
Heat Map
ColData pheatmap DESeq2
written 2.4 years ago by • 0
1
vote
6
replies
3.2k
views
Choosing between VST and rlog for PCA for outlier identification in DESeq2 when small number of samples
DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
3
replies
1.1k
views
Normalization of different input materials
Normalization DESeq2
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 10
3
votes
2
replies
1.2k
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 30
4,839 results • Page 11 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, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
United States, 1 hour ago
United States, 1 hour ago
United States, 2 hours ago
Traffic: 678 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