Showing : DEseq2 • reset
0
votes
2
replies
2.2k
views
error in file(file, "rt") when reading in sample sheet using DESeqDataSetFromHTSeqCount
DESeq2
4.4 years ago Yihan • 0
1
vote
2
replies
1.0k
views
Doing multiple comparisons in a DESeq2 object with multiple conditions
DESeq2
4.4 years ago jenabris • 0
3
votes
16
replies
3.8k
views
DESeq2 - groups with biological replicates from the same patient
DESeq2
updated 22 months ago by 4.2k • written 4.4 years ago by ▴ 10
0
votes
4
replies
2.8k
views
estimateSizeFactors throws "Error in .local(object, ..., value) : all(!is.na(value)) is not TRUE". Identified root cause within estimateSizeFactorsFo…
DESeq2
4.4 years ago alawrence2211 • 0
3
votes
4
replies
4.7k
views
Clarification re VST transformed data in DESeq2
DESeq2
updated 4.4 years ago by ★ 5.0k • written 4.4 years ago by • 0
0
votes
1
reply
1.4k
views
DESseq2 question about VST and rlog
DESeq2 Normalization
updated 4.4 years ago by ★ 5.0k • written 4.4 years ago by • 0
2
votes
1
reply
993
views
estimateSizeFactors before or after removing non-coding genes and filtering for low counts
DESeq2 RNASeq
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
3
votes
3
replies
1.8k
views
How is DESeq2 handling replicates?
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by ▴ 10
0
votes
6
replies
1.5k
views
Bias of lowly expressed genes in DESeq2
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
votes
2
replies
2.5k
views
DESeq2 for longitudinal data
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
votes
3
replies
947
views
Highly left- skewed raw pvalues from DESeq2 analysis
DESeq2
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
0
votes
6
replies
1.3k
views
DESeq2 time course confusion
DESeq2 DifferentialExpression
4.4 years ago rajpal22288 ▴ 10
2
votes
2
replies
891
views
dispersion increasing for extreme high mean counts
DESeq2
4.4 years ago XTR5 ▴ 10
0
votes
2
replies
1.9k
views
Install older version of DESeq2 for use on cluster with older version of R
DESeq2 BiocVersion
updated 4.4 years ago by • 0 • written 4.4 years ago by • 0
1
vote
5
replies
2.6k
views
how to plot multiple RLEs on same plot?
plotRLE Nanostring RUVSeq DESEQ2
updated 15 months ago by ▴ 70 • written 4.4 years ago by ▴ 60
1
vote
1
reply
1.4k
views
DESeq2 for allele-specific expression with contrasts between conditions
DESeq2 AllelicImbalance edgeR RNASeq
updated 4.4 years ago by 43k • written 4.4 years ago by • 0
1
vote
3
replies
1.4k
views
DESeq2: NA's in mcols(object)$betaConv
DESeq2
updated 4.4 years ago by 43k • written 4.5 years ago by • 0
0
votes
2
replies
729
views
DESeq2: One or more designs for contrasts of interest
DESeq2
4.5 years ago • updated 4.4 years ago Mirin1357 • 0
2
votes
2
replies
2.4k
views
DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
4.5 years ago • updated 4.4 years ago SUMIT • 0
0
votes
2
replies
2.4k
views
PCA and heatmaps: most variable genes selection
DESeq2 ExpressionData heatmaps pca
4.5 years ago Clara ▴ 10
2
votes
6
replies
6.1k
views
Salmon, RUVSeq and DESeq2
Salmon DESeq2 DEG RUVSeq
4.5 years ago • updated 4.4 years ago reganhayward • 0
3
votes
5
replies
4.3k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 60
0
votes
7
replies
1.5k
views
matrix with Salmon gene-level quantifications in DESeq
DESeq2
4.5 years ago • updated 4.4 years ago luca.s ▴ 50
0
votes
8
replies
2.9k
views
DESeq2: Variable Importance
DESeq2 RNASeq
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
votes
1
reply
765
views
DESeq2 - how to account for patient, batch and condition
DESeq2
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 10
2
votes
4
replies
1.8k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 2.2 years ago by 43k • written 4.5 years ago by • 0
0
votes
9
replies
2.6k
views
Why is my plot count does not fit with log fold change result?
DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 30
0
votes
4
replies
1.1k
views
Number of genes differs between two design formulas in deseq2
DESeq2
4.5 years ago Mohamed Malek • 0
1
vote
6
replies
2.6k
views
Statistics on normalized counts
DESeq2
updated 4.5 years ago by • 0 • written 4.5 years ago by • 0
0
votes
3
replies
1.9k
views
[DEseq2] How to properly add a noise coefficient to the experiment design formula
limma edgeR DEseq2
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 30
1
vote
1
reply
1.0k
views
DESeq2 - DGE in organoids for multiple group comparisons
personalome organoids DGE DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 10
0
votes
1
reply
726
views
Why is the number of DEG different when comparing A versus B and B versus A?
DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
0
votes
2
replies
1.4k
views
where to download practice data
DESeq2
updated 4.5 years ago by ★ 5.0k • written 4.5 years ago by • 0
0
votes
1
reply
979
views
DESeq2: Paired samples (before and after treatment) with different responses
DESeq2
updated 4.5 years ago by ★ 1.4k • written 4.5 years ago by • 0
2
votes
2
replies
908
views
How to remove batch effect from multiple rna-seq dataset before running deseq2
DESeq2
4.5 years ago Yosapol • 0
0
votes
1
reply
1.6k
views
Creating a DESeqDataSet from a RangedSummarizedExperiment - where is the design parameter in RangedSummarizedExperiment
SRA DESeq2
4.5 years ago Serge • 0
0
votes
3
replies
1.4k
views
Contrasting LogFCs in DESeq2
DESeq2 RNASeqData
updated 4.5 years ago by ★ 1.4k • written 4.5 years ago by • 0
1
vote
1
reply
1.7k
views
[DESeq2] - Making DESeq Dataset object from csv of already normalized counts.
DESeq2
4.5 years ago Michael • 0
0
votes
2
replies
806
views
DESeq2 - Cannot replicate log2FC calculations
DESeq2
4.5 years ago Sara • 0
2
votes
2
replies
2.3k
views
DESeq2 time-series with two conditions and several patients
DESeq2
4.5 years ago Karolina Trachtova ▴ 10
1
vote
2
replies
2.2k
views
Design Formula, PCA, and Sex Effect
DESeq2
4.5 years ago GHI ▴ 10
0
votes
5
replies
1.8k
views
Tximport/DESeq2 Normalization Process
tximport Normalization DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
4
votes
3
replies
2.1k
views
Concatenating expression counts from different RNA-seq quantification tools
tximport HERVs edgeR DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by ▴ 40
0
votes
1
reply
1.2k
views
FDR Correction
dada2 Metagenomics DESeq2
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
2
votes
8
replies
3.0k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
4.5 years ago Jane ▴ 10
6
votes
12
replies
3.1k
views
ColData use only certain variable within
DESeq2
4.5 years ago Bine ▴ 50
0
votes
2
replies
2.0k
views
Error in DESeqDataSetFromMatrix()
DESeq2 RNAseq
updated 3.4 years ago by ▴ 10 • written 4.5 years ago by • 0
1
vote
2
replies
3.5k
views
Plotting FPKM
ggplots2 DESeq2 fpkm()
4.5 years ago GA ▴ 10
1
vote
4
replies
1.1k
views
Incorrect 2-fold change reported in DESeq2 Data
DESeq2
4.5 years ago Naphtap92 ▴ 10
0
votes
3
replies
2.0k
views
Can't install DESeq2 because of libxml
deseq2 libxml xml
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
4,839 results • Page 29 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 Gordon Smyth 53k
Popular Question to shepherl 4.2k
Popular Question to story.benjamin ▴ 20
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Locations • All
Germany, 51 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
Switzerland, 5 hours ago
Barcelona, Spain, 6 hours ago
The city by the bay, 8 hours ago
Traffic: 846 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