Showing : deseq2 • reset
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1.2k
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
23 months ago Karthik • 0
0
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3
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2.6k
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DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values in assay are negative
RNASeqData DESeq2
23 months ago Oenone • 0
1
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1
reply
596
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Lower FDR cutoff gives more gene counts
DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
1
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1
reply
746
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Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
1
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1
reply
714
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Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
0
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1
reply
777
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How to use DESeq results with LRT vs. with Wald's test
DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
0
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1
reply
826
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DEseq2 : Complex design with a mixture of male and female mice
statistics DESeq2
updated 23 months ago by 43k • written 23 months ago by • 0
0
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2
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1.3k
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Help Subsetting DDS for plotPCA for contrast groups
Rstudio plotPCA DESeq2
23 months ago yee • 0
0
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2
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956
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Batch correction where one of the batches only has a single sample
DESeq2
23 months ago Tom ▴ 10
0
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3
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1.1k
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Deseq2 - Pairwise results from 6 conditions - error non-conformable arguments
DESeq2
23 months ago claire • 0
2
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3
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1.5k
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
23 months ago Karthik • 0
0
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1
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767
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 23 months ago by 43k • written 23 months ago by ▴ 10
2
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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
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4
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1.4k
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Can DESeq2 be used to compare groups of genes?
DESeq2
23 months ago pl23 • 0
2
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2
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1.1k
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Predicting missing values splines DESeq2
deseq DESeq2
23 months ago georgii.vdovin • 0
0
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1
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572
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DESeq2 design with unbalance data and a multifactor design
DESeq2
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
0
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2
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1.3k
views
DESeq2 for microbiome data: raw counts or percentages?
microbiome DESeq2
23 months ago anton.kratz ▴ 60
0
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1
reply
863
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DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 23 months ago by ★ 13k • written 23 months ago by • 0
4
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9
replies
2.1k
views
DESeq2 unable to handle large count values
DESeq2
updated 12 months ago by 43k • written 24 months ago by • 0
2
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5
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2.5k
views
SparseArray unable to install on Bioc 3.18
DESeq2 SummarizedExperiment SparseArray Install DelayedArray
updated 24 months ago by 43k • written 24 months ago by • 0
0
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1
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789
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DESeq2 model for two genome system
RNASeq DESeq2
updated 24 months ago by 43k • written 2.0 years ago by • 0
0
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1
reply
881
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DESeq2: different results with and without releveling when providing contrast
DESeq2
updated 24 months ago by 43k • written 24 months ago by • 0
0
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1
reply
803
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 24 months ago by 43k • written 24 months ago by • 0
0
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2
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940
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Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
24 months ago Ben ▴ 10
0
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9
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3.2k
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DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 24 months ago by • 0 • written 8.0 years ago by ▴ 60
0
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2
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2.6k
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MA plot for DESEq2 analysis
RNASeqData DESeq2
24 months ago RHEA • 0
1
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1
reply
593
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DESeqResults object -> extract statistics results with rownames (gene)
DESeq2
updated 24 months ago by ★ 5.0k • written 24 months ago by ▴ 50
0
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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 68k • written 24 months ago by • 0
0
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3
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866
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DESeq2: FPMs varying based on sample groups used
DESeq2
updated 24 months ago by ★ 5.0k • written 24 months ago by • 0
0
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8
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1.6k
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
24 months ago Luca • 0
0
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1
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2.6k
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Error when trying to create a heatmap with DESeq2
Heatmap RNA-seqanalysis heatmaps DESeq2
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by • 0
2
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10
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2.4k
views
Accounting for Batch effect reduces DEGs drastically
DESeq2
2.0 years ago • updated 24 months ago rohitsatyam102 ▴ 20
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6
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2.3k
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
2.0 years ago erika.maldonado-rosado • 0
0
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2
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979
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How can I devise a method like DESeq2 to give statistics for paired multiple -omic datasets?
DESeq2
updated 2.0 years ago by • 0 • written 2.0 years ago by • 0
0
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4
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1.4k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 18 months ago by 43k • written 2.0 years ago by • 0
2
votes
3
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2.6k
views
Two factor design including interaction effect with DESeq2 in R
DESeq2 RNASeqData deseq2 ExperimentalDesign
updated 2.0 years ago by ★ 1.4k • written 2.0 years ago by • 0
0
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2
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738
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DESeq2: how could the lower mean abundance treatment show a positive and significant LFC?
DESeq2
2.0 years ago Roey Angel • 0
0
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2
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1.1k
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Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
2.0 years ago Karthik • 0
0
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1
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1.8k
views
DESeq2 Error in Results Contrast and ResultsNames
DESeq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
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0
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712
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
2.0 years ago Florian • 0
0
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1
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2.2k
views
choosing rank for GSEA
gsea DESeq2
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
1
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1
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1.0k
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
0
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3
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1.2k
views
Tximport Error - transcripts in quant files are not the same as tx2gene
salmon tximport deseq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
1
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11
replies
2.9k
views
DESeq2 gene length normalisation
Normalization DESeq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
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2
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1.1k
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Differential Expression Cutoffs for n = 1
clusterProfiler DESeq2
2.0 years ago georgii.vdovin • 0
3
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5
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1.7k
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DESeq2: Design model includes sex but only one female
DESeq2
updated 2.0 years ago by 43k • written 2.0 years ago by • 0
0
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1
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1.7k
views
DeSeq2 normalization 16S
DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
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4
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1.4k
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
2.1 years ago • updated 2.0 years ago ar14g12 • 0
0
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2
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824
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Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 0
0
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1
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891
views
DeSeq2 data comparison and extracting outputs
DESeq2
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by • 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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