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DeSeq2
•
reset
0
votes
4
replies
137
views
Identical samples after deseq2 batch effect removal
DESeq2
19 hours ago • updated 10 minutes ago
maripane
• 0
0
votes
1
reply
110
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 13 hours ago by
James W. MacDonald
67k • written 15 hours ago by
rj1435
• 0
1
vote
2
replies
166
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
1 day ago • updated 20 hours ago
Denise
• 0
0
votes
1
reply
76
views
eRNAs count
RNASeq
DESeq2
updated 3 days ago by
ATpoint
★ 4.5k • written 3 days ago by
Irene
• 0
0
votes
1
reply
340
views
DESeq2 rerun returns different results
DESeq2
updated 7 days ago by
ATpoint
★ 4.5k • written 7 days ago by
wl1111
• 0
0
votes
1
reply
170
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
145
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
519
views
Handling biological replicates in DESeq2
DESeq2
updated 9 days ago by
ATpoint
★ 4.5k • written 10 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
861
views
Volcano plot has many values around zero
RNA-seq
DESeq2
volcanoplot
updated 13 days ago by
Michael Love
42k • written 13 days ago by
nramakr
▴ 10
0
votes
2
replies
322
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 15 days ago by
ballackselma
• 0
4
votes
5
replies
564
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
17 days ago • updated 16 days ago
LuciaNhu
• 0
0
votes
1
reply
357
views
Average expression of genes across replicates
DESeq2
updated 19 days ago by
ATpoint
★ 4.5k • written 20 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
312
views
Deseq to output continous sequencing data
DESeq2
updated 24 days ago by
Michael Love
42k • written 5 weeks ago by
Neha
• 0
1
vote
4
replies
735
views
Adjusted p-values become NA when sub-setting samples
DESeq2
6 weeks ago • updated 15 days ago
txema.heredia
• 0
3
votes
3
replies
828
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma
edgeR
DESeq2
MAST
written 26 days ago by
Satoshi
• 0
0
votes
2
replies
317
views
ESTMATE, MCPcounter, EPIC, xCell input
DESeq2
ESTIMATE
RNASeqData
MCPcounter
written 4 weeks ago by
Aleksandra
• 0
0
votes
1
reply
265
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
718
views
DESeq2 - interactions when using factors concatenated into group
DESeq2
5 weeks ago • updated 27 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
184
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
454
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 7 weeks ago by
Ricardo Iván
• 0
0
votes
1
reply
166
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
785
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
424
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
265
views
RNA-Seq p value range variation
DESeq2
pvalue
RNA-Seq
6 weeks ago
paul.meraner
• 0
0
votes
0
replies
177
views
News:
RNAseq data analysis with Bioconductor (online course)
DESeq2
SummarizedExperiment
6 weeks ago • updated 22 days ago
info
▴ 10
0
votes
5
replies
543
views
heatmap with batch effect
DESeq2
BatchEffect
7 weeks ago • updated 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
226
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
318
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
433
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
688
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
487
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
690
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 9 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
Answer: Identical samples after deseq2 batch effect removal
by
maripane
• 0
Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…
Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
by
rcreed
• 0
The updated version worked well on my data. Thank you!
Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di
by
James W. MacDonald
67k
The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…
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…
Votes
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
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
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