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DESEq2
•
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0
votes
0
replies
4
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
20 minutes ago
rj1435
• 0
0
votes
3
replies
52
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 20 minutes ago by
Michael Love
42k • written 4 hours ago by
maripane
• 0
1
vote
2
replies
158
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
1 day ago • updated 5 hours ago
Denise
• 0
0
votes
1
reply
74
views
eRNAs count
RNASeq
DESeq2
updated 3 days ago by
ATpoint
★ 4.5k • written 3 days ago by
Irene
• 0
0
votes
1
reply
338
views
DESeq2 rerun returns different results
DESeq2
updated 6 days ago by
ATpoint
★ 4.5k • written 6 days ago by
wl1111
• 0
0
votes
1
reply
168
views
Is my time course analysis with DESeq2 valid?
GeneExpression
DESeq2
TimeCourse
updated 7 days ago by
Michael Love
42k • written 8 days ago by
Jason
• 0
0
votes
1
reply
140
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2
deseq
updated 9 days ago by
Guido Hooiveld
★ 4.1k • written 9 days ago by
Najla Abassi
• 0
2
votes
2
replies
518
views
Handling biological replicates in DESeq2
DESeq2
updated 9 days ago by
ATpoint
★ 4.5k • written 9 days ago by
sk
• 0
5
votes
2
replies
25k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
written 5.9 years ago by
aishu.jp
▴ 30
1
vote
6
replies
860
views
Volcano plot has many values around zero
RNA-seq
DESeq2
volcanoplot
updated 12 days ago by
Michael Love
42k • written 12 days ago by
nramakr
▴ 10
0
votes
2
replies
319
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 15 days ago by
ballackselma
• 0
4
votes
5
replies
563
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
16 days ago
LuciaNhu
• 0
0
votes
1
reply
356
views
Average expression of genes across replicates
DESeq2
updated 18 days ago by
ATpoint
★ 4.5k • written 19 days ago by
James
• 0
0
votes
0
replies
101
views
News:
RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2
GenomicRanges
22 days ago
info
▴ 10
0
votes
10
replies
1.2k
views
Question about using LRT test for time course experiments with DESeq2
DESeq2
23 days ago • updated 16 days ago
Denise
• 0
0
votes
1
reply
310
views
Deseq to output continous sequencing data
DESeq2
updated 23 days ago by
Michael Love
42k • written 5 weeks ago by
Neha
• 0
1
vote
4
replies
733
views
Adjusted p-values become NA when sub-setting samples
DESeq2
5 weeks ago • updated 14 days ago
txema.heredia
• 0
3
votes
3
replies
827
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 25 days ago by
Satoshi
• 0
0
votes
2
replies
313
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2
ESTIMATE
RNASeqData
MCPcounter
written 4 weeks ago by
Aleksandra
• 0
0
votes
1
reply
264
views
Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
nicolettacommins
• 0
2
votes
3
replies
984
views
Analysis of large RNA-Seq Datasets
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
KokiBio
• 0
1
vote
4
replies
716
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
4 weeks ago • updated 26 days ago
boczniak767
▴ 740
0
votes
1
reply
180
views
2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
5 weeks ago
JY
• 0
0
votes
1
reply
259
views
How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 5 weeks ago by
Michael Love
42k • written 5 weeks ago by
agamemnon
• 0
0
votes
2
replies
187
views
how to extract expression matrix post deseq2
DESeq2
written 5 weeks ago by
agamemnon
• 0
0
votes
2
replies
183
views
Using Normalized Counts in DESeq2
DESeq2
updated 5 weeks ago by
Michael Love
42k • written 5 weeks ago by
KokiBio
• 0
1
vote
2
replies
227
views
When running contrasts, does it use normalized read counts?
DESeq2
5 weeks ago
Katherine
• 0
0
votes
1
reply
183
views
How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 5 weeks ago by
swbarnes2
★ 1.4k • written 5 weeks ago by
Bingqian
• 0
3
votes
4
replies
453
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization
DESeq2
rlog
vst
5 weeks ago
Eva
▴ 10
1
vote
4
replies
461
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq
DESeq2
Oddresults
updated 5 weeks ago by
ATpoint
★ 4.5k • written 6 weeks ago by
Ricardo Iván
• 0
0
votes
1
reply
165
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression
ImpulseDE2
DESeq2
updated 6 weeks ago by
Michael Love
42k • written 6 weeks ago by
Jay
• 0
3
votes
11
replies
696
views
Highly DE genes but small count difference within conditions
RNASeq
DESeq2
RNASeqData
written 6 weeks ago by
bioshot.com
• 0
2
votes
4
replies
386
views
RNASeq Time Course Question
DESeq2
RNASeq
TimeCourse
6 weeks ago
jihoon.kim.1495
▴ 10
0
votes
6
replies
783
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression
DESeq2
BatchEffect
updated 26 days ago by
Michael Love
42k • written 6 weeks ago by
CriticalPeriod
• 0
5
votes
4
replies
423
views
How to control batch effect if Group and batch are same?
limma
DESeq2
BatchEffect
updated 6 weeks ago by
ATpoint
★ 4.5k • written 7 weeks ago by
Bioinformagician
• 0
0
votes
2
replies
264
views
RNA-Seq p value range variation
DESeq2
pvalue
RNA-Seq
6 weeks ago
paul.meraner
• 0
0
votes
0
replies
175
views
News:
RNAseq data analysis with Bioconductor (online course)
DESeq2
SummarizedExperiment
6 weeks ago • updated 22 days ago
info
▴ 10
0
votes
5
replies
541
views
heatmap with batch effect
DESeq2
BatchEffect
6 weeks ago
tothuhien
• 0
0
votes
2
replies
342
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport
DESeq2
updated 7 weeks ago by
Michael Love
42k • written 7 weeks ago by
oguzhankaraosmanoglu
• 0
1
vote
1
reply
253
views
Deseq2 sfType
Microbiome
DESeq2
RNASeq
updated 7 weeks ago by
James W. MacDonald
67k • written 7 weeks ago by
Caroline
• 0
1
vote
1
reply
225
views
Normalization RNA-seq for multiple plates
Normalization
DESeq2
RNASeqData
edgeR
updated 7 weeks ago by
ATpoint
★ 4.5k • written 7 weeks ago by
Pimpa
• 0
1
vote
1
reply
317
views
DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 7 weeks ago by
ATpoint
★ 4.5k • written 7 weeks ago by
picasa1983
• 0
1
vote
2
replies
432
views
Poor dispersion fit in DESeq2
limma
DESeq2
RNASeq
edgeR
updated 7 weeks ago by
Michael Love
42k • written 8 weeks ago by
Ben
▴ 10
0
votes
2
replies
687
views
DESeq2 analysis on 2 plant lines infected with virus, with 2 time points (days post infection)
DESeq2
updated 7 weeks ago by
Michael Love
42k • written 8 weeks ago by
duplessisantzel
• 0
1
vote
2
replies
486
views
DESeq2 design and contrasts with 2 drug-treated and one control group
DESeq2
Bioconductor
updated 7 weeks ago by
Michael Love
42k • written 9 weeks ago by
JT
▴ 10
1
vote
6
replies
687
views
New to Deseq2 - DEG questions / MA plot
genomes
DESeq2
Transcriptomics
updated 4 weeks ago by
ATpoint
★ 4.5k • written 8 weeks ago by
Newbie
• 0
0
votes
1
reply
287
views
Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)?
DESeq2
updated 8 weeks ago by
Michael Love
42k • written 8 weeks ago by
madivinakristidiscar
• 0
17
votes
9
replies
7.0k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 9 weeks ago by
James W. MacDonald
67k • written 8.5 years ago by
ompandey
▴ 10
0
votes
1
reply
278
views
Dealing with 0 miRNA counts in DESeq2 analysis and influence in adjusted p-value
microRNAome
DESeq2
updated 9 weeks ago by
Michael Love
42k • written 9 weeks ago by
eric
• 0
0
votes
2
replies
496
views
PCA analysis RNA-Seq QC looks strange?
DESeq2
updated 10 weeks ago by
swbarnes2
★ 1.4k • written 11 weeks ago by
Megan
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Identical samples after deseq2 batch effect removal
by
Michael Love
42k
Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…
Comment: Identifying potentially associated gene set to drug response using GSVA
by
Kent
• 0
Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
by
James W. MacDonald
67k
You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…
Answer: HilBertVis install error
by
James W. MacDonald
67k
It appears you have compiler flags set that preclude you from compiling (-Werror=format-security). If I install `HilbertVis` on my work box…
Comment: Identical samples after deseq2 batch effect removal
by
maripane
• 0
Thanks Michael for quick reply. Actually, I also questioned this but later i saw this issue happens within another cluster and different c…
Votes
A: TopGO: How to retrieve the gene list related to a GO ID ?
A: Error in DESeqDataSet : some values in assay are not integers
A: correcting the batch effects in Limma and SVA
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
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