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deseq2
•
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0
votes
3
replies
1.2k
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
23 months ago
Karthik
• 0
0
votes
3
replies
2.6k
views
DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData
DESeq2
23 months ago
Oenone
• 0
1
vote
1
reply
596
views
Lower FDR cutoff gives more gene counts
DESeq2
updated 23 months ago by
Michael Love
43k • written 23 months ago by
Binjie
• 0
1
vote
1
reply
746
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq
DESeq2
updated 23 months ago by
Michael Love
43k • written 23 months ago by
pl23
• 0
1
vote
1
reply
714
views
Limma/DESeq2 for unbalanced nested design (paired samples)
limma
DESeq2
updated 23 months ago by
Michael Love
43k • written 23 months ago by
michael.eigenschink
• 0
0
votes
1
reply
777
views
How to use DESeq results with LRT vs. with Wald's test
DESeq2
updated 23 months ago by
Michael Love
43k • written 23 months ago by
luise.bellach
• 0
0
votes
1
reply
826
views
DEseq2 : Complex design with a mixture of male and female mice
statistics
DESeq2
updated 23 months ago by
Michael Love
43k • written 23 months ago by
lionel.spinelli
• 0
0
votes
2
replies
1.3k
views
Help Subsetting DDS for plotPCA for contrast groups
Rstudio
plotPCA
DESeq2
23 months ago
yee
• 0
0
votes
2
replies
956
views
Batch correction where one of the batches only has a single sample
DESeq2
23 months ago
Tom
▴ 10
0
votes
3
replies
1.1k
views
Deseq2 - Pairwise results from 6 conditions - error non-conformable arguments
DESeq2
23 months ago
claire
• 0
2
votes
3
replies
1.5k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq
DESeq2
23 months ago
Karthik
• 0
0
votes
1
reply
767
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData
DifferentialExpression
DESeq2
updated 23 months ago by
Michael Love
43k • written 23 months ago by
Pez
▴ 10
2
votes
2
replies
1.0k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression
DESeq2
RNASeqData
RNASeq
StatisticalMethod
23 months ago
Manthos
• 0
1
vote
4
replies
1.4k
views
Can DESeq2 be used to compare groups of genes?
DESeq2
23 months ago
pl23
• 0
2
votes
2
replies
1.1k
views
Predicting missing values splines DESeq2
deseq
DESeq2
23 months ago
georgii.vdovin
• 0
0
votes
1
reply
572
views
DESeq2 design with unbalance data and a multifactor design
DESeq2
updated 23 months ago by
ATpoint
★ 5.0k • written 23 months ago by
ari.bo
• 0
0
votes
2
replies
1.3k
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome
DESeq2
23 months ago
anton.kratz
▴ 60
0
votes
1
reply
863
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData
DESeq2
updated 23 months ago by
Wolfgang Huber
★ 13k • written 23 months ago by
meroy
• 0
4
votes
9
replies
2.1k
views
DESeq2 unable to handle large count values
DESeq2
updated 12 months ago by
Michael Love
43k • written 24 months ago by
robennet
• 0
2
votes
5
replies
2.5k
views
SparseArray unable to install on Bioc 3.18
DESeq2
SummarizedExperiment
SparseArray
Install
DelayedArray
updated 24 months ago by
Michael Love
43k • written 24 months ago by
eg226
• 0
0
votes
1
reply
789
views
DESeq2 model for two genome system
RNASeq
DESeq2
updated 24 months ago by
Michael Love
43k • written 2.0 years ago by
Sean
• 0
0
votes
1
reply
881
views
DESeq2: different results with and without releveling when providing contrast
DESeq2
updated 24 months ago by
Michael Love
43k • written 24 months ago by
drew
• 0
0
votes
1
reply
803
views
Controling for Covariates With a Continuous Predictor Variable
Deseq
DESeq2
updated 24 months ago by
Michael Love
43k • written 24 months ago by
georgii.vdovin
• 0
0
votes
2
replies
940
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData
DESeq2
24 months ago
Ben
▴ 10
0
votes
9
replies
3.2k
views
DESeq2 result really different when only use some sample vs all sample
deseq2
rnaseq
updated 24 months ago by
blowfish
• 0 • written 8.0 years ago by
bharata1803
▴ 60
0
votes
2
replies
2.6k
views
MA plot for DESEq2 analysis
RNASeqData
DESeq2
24 months ago
RHEA
• 0
1
vote
1
reply
593
views
DESeqResults object -> extract statistics results with rownames (gene)
DESeq2
updated 24 months ago by
ATpoint
★ 5.0k • written 24 months ago by
Bine
▴ 50
0
votes
7
replies
4.3k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error
RStudio
ggplot2
DESeq2
updated 24 months ago by
James W. MacDonald
68k • written 24 months ago by
BioES
• 0
0
votes
3
replies
866
views
DESeq2: FPMs varying based on sample groups used
DESeq2
updated 24 months ago by
ATpoint
★ 5.0k • written 24 months ago by
Jay
• 0
0
votes
8
replies
1.6k
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression
DESeq2
24 months ago
Luca
• 0
0
votes
1
reply
2.6k
views
Error when trying to create a heatmap with DESeq2
Heatmap
RNA-seqanalysis
heatmaps
DESeq2
updated 2.0 years ago by
Basti
▴ 780 • written 2.0 years ago by
langziv
• 0
2
votes
10
replies
2.4k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
2.0 years ago • updated 24 months ago
rohitsatyam102
▴ 20
0
votes
6
replies
2.3k
views
DESeq2 Normalization with 4 Groups
Normalization
RNASeq
DESeq2
2.0 years ago
erika.maldonado-rosado
• 0
0
votes
2
replies
979
views
How can I devise a method like DESeq2 to give statistics for paired multiple -omic datasets?
DESeq2
updated 2.0 years ago by
edammer
• 0 • written 2.0 years ago by
Christina
• 0
0
votes
4
replies
1.4k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 18 months ago by
Michael Love
43k • written 2.0 years ago by
Crystal571
• 0
2
votes
3
replies
2.6k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2
RNASeqData
deseq2
ExperimentalDesign
updated 2.0 years ago by
swbarnes2
★ 1.4k • written 2.0 years ago by
Sam
• 0
0
votes
2
replies
738
views
DESeq2: how could the lower mean abundance treatment show a positive and significant LFC?
DESeq2
2.0 years ago
Roey Angel
• 0
0
votes
2
replies
1.1k
views
Will DESeq2 be appropriate tool for analysis?
RNASeq
DESeq2
2.0 years ago
Karthik
• 0
0
votes
1
reply
1.8k
views
DESeq2 Error in Results Contrast and ResultsNames
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
J_Can
• 0
0
votes
0
replies
712
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
2.0 years ago
Florian
• 0
0
votes
1
reply
2.2k
views
choosing rank for GSEA
gsea
DESeq2
updated 2.0 years ago by
ATpoint
★ 5.0k • written 2.0 years ago by
Grace.Ciabattoni
• 0
1
vote
1
reply
1.0k
views
Multiple comparison using DESeq2
RNASeqData
RNASeq
DESeq2
updated 2.0 years ago by
James W. MacDonald
68k • written 2.0 years ago by
fuqichen1
• 0
0
votes
3
replies
1.2k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon
tximport
deseq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
Kayleigh
• 0
1
vote
11
replies
2.9k
views
DESeq2 gene length normalisation
Normalization
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
cm15245
• 0
0
votes
2
replies
1.1k
views
Differential Expression Cutoffs for n = 1
clusterProfiler
DESeq2
2.0 years ago
georgii.vdovin
• 0
3
votes
5
replies
1.7k
views
DESeq2: Design model includes sex but only one female
DESeq2
updated 2.0 years ago by
Michael Love
43k • written 2.0 years ago by
mphogan
• 0
0
votes
1
reply
1.7k
views
DeSeq2 normalization 16S
DESeq2
updated 2.1 years ago by
Michael Love
43k • written 2.1 years ago by
Alexis
• 0
0
votes
4
replies
1.4k
views
DESeq2 : standardising variation between treatments
RNA-seq
DESeq2
2.1 years ago • updated 2.0 years ago
ar14g12
• 0
0
votes
2
replies
824
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality
RNASeq
DESeq2
updated 2.1 years ago by
swbarnes2
★ 1.4k • written 2.1 years ago by
Jules
• 0
0
votes
1
reply
891
views
DeSeq2 data comparison and extracting outputs
DESeq2
updated 2.1 years ago by
swbarnes2
★ 1.4k • written 2.1 years ago by
sedabarutcu.a
• 0
4,835 results • Page
9 of 97
Recent ...
Replies
Comment: deseq2 filter the low counts
by
empty_mt
• 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
by
dan.gatti
• 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions
by
Michael Love
43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed
by
shepherl
4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Comment: bake() and cool() resulting in an empty table
by
Francesc
• 0
Hi Catherine, thanks so much for using dar and for reporting this bug! We have identified the issue and pushed a fix to the dar repo (PR #…
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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