Showing : DESEq2 • reset
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DESeq2 analysis with multiple factors
DESeq2 DEG multiplefactors deseq2
updated 6.1 years ago by ★ 13k • written 6.1 years ago by • 0
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1
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753
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DESeq2 - lfcShrink reversing sign for all logFCs - clarification on "contrast" argument?
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
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4
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1.4k
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write.table of DESeq2 results broken down by LFC
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 60
1
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1
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538
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Differential gene expression analysis
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
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4
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2.2k
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Difference in PCA variance calculation in DESeq2
deseq2 pca hclust
updated 6.1 years ago by 43k • written 6.1 years ago by ▴ 80
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5
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1.9k
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tximeta link to transcriptome
deseq2
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
1
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6
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1.7k
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Paired t-test with DESeq2
deseq2
updated 6.1 years ago by ★ 1.4k • written 6.1 years ago by ▴ 30
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4
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2.4k
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DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
6.2 years ago • updated 6.1 years ago luciest.rodriguez • 0
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4
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2.5k
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DESeq2 using many cores despite parallel = FALSE
deseq2 parallel
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
8
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18
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17k
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Batch correction by using ComBat function in sva package
deseq2 combat Knownbatcheffect Tutorial
updated 4.8 years ago by • 0 • written 6.2 years ago by ▴ 10
2
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2
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2.1k
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Modelling a multiplicative batch effect with DESeq2
deseq2 batch-effects ComBat
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
3
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6
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3.0k
views
Repeated measures per individual and unbalanced number of measures per individual: DE between groups still an ordinary two-group comparison?
differentialexpression deseq2 limma edger repeatedmeasures
6.2 years ago • updated 3.9 years ago hermidalc ▴ 20
3
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4
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1.2k
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DESeq2 VS edgeR DEG results different in analysis same data
DESeq2 edgeR
updated 6.2 years ago by 53k • written 6.2 years ago by ▴ 10
2
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4
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1.1k
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Combining RSEM Files with dif row # for tximport
tximport DEseq2 RNAseq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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6
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3.0k
views
Batch effects between different sequencing runs
deseq2 batchcorrection
updated 6.2 years ago by ★ 1.4k • written 6.2 years ago by ▴ 60
3
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3
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1.2k
views
DESeq2 lfcshrink generate 0 svalues
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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3
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1.5k
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DESeq2 time course with two genotypes
deseq2 timecourse michael love multiple time points
6.2 years ago cp1015 • 0
2
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5
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2.2k
views
SVA for repeated measures design
SVA deseq2 repeated measures
updated 6.2 years ago by ★ 3.4k • written 6.2 years ago by • 0
4
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10
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2.2k
views
DeSeq2 Design (A-B)-(C-D)
deseq2 limma
updated 6.2 years ago by 53k • written 6.2 years ago by ▴ 30
0
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1
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1.7k
views
Using RUVs on Deseq2 but clustering still seems wrong
deseq2 ruv batch
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
3
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3
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1.4k
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DESeq2 indirect batch effect removal
deseq2 batch
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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6
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3.2k
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Extracting VST matrix with batch effects removed
deseq2 batchcorrection
6.2 years ago A ▴ 60
2
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1
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3.3k
views
How to perform a differential expression analysis from TCGA file EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv
cancer limma deseq2
updated 6.2 years ago by ▴ 840 • written 6.2 years ago by ▴ 20
2
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6
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992
views
Deseq metadata bug on repeat runs with parallel
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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3
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713
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DESeq2 Identical P values in both standard and multi factor design
deseq2 r
6.2 years ago dtlloyd • 0
6
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19
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5.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 19 months ago by • 0 • written 6.2 years ago by ▴ 10
1
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1
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1.4k
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DESeq Normalisation, miRNASeq
deseq2 normalization miRNASeq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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5
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782
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Differential expression analyses
normalization deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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4
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1.2k
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DESeq2: Internal reference and multiple comparisons
deseq2
updated 6.2 years ago by • 0 • written 6.2 years ago by • 0
0
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4
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1.0k
views
non-significant p-values from DESeq2 for some genes, visually the data looks significant
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
1
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3
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2.1k
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delete samples from summarizedExperiment
deseq2
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
3
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2
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2.8k
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Variation between technical replicates (DESeq2, batch effects)
rnaseq deseq2 differential expression batch effect replicates
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
1
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8
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1.1k
views
high lcfSE for genes with zero counts in the majority of conditions
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
1
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3
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1.2k
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DESeq2 very high log2foldchange values
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
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2
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940
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rlog() is not working ?
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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4
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1.5k
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DESeq2 - controlling for block vs analysing blocks separately and lfcShrink changes the DE genes drastically
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 20
0
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6
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1.1k
views
DESeq2 design for paired samples 'Model matrix not full rank'
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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11
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1.9k
views
DEseq2 design for knockdown conditions and treatment
deseq2
updated 6.2 years ago by ★ 1.4k • written 6.2 years ago by • 0
1
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2
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1.5k
views
Normalizing counts using TIN metric before DESeq2
deseq2 tximport salmon
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
6
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5
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1.9k
views
DESeq2 lfcShrink and unshrunk fold changes
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 50
0
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1
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840
views
51 views DESeq2 RNAseq differential expression analysis
deseq2 likelihood ratio rna seq wald test
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
1
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8
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1.1k
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Responder Vs Non-Responders Paired Comparison DESeq2
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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1
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1.5k
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Handling adjustment variables and surrogate variables in model
sva deseq2
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
1
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3
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4.4k
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Multi-factor analysis Deseq2
deseq2 contrast LTR
7.1 years ago • updated 6.2 years ago Iryna • 0
1
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1
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1.1k
views
DESeq2 RNAseq differential expression analysis
deseq2 rnaseq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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5
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1.4k
views
FPM value and batch correction
deseq2 limma
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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18
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4.5k
views
Subset-ing Large DESeqDataSet for data extraction with contrast function
deseq2
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
2
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3
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2.1k
views
Deseq2 post functional annotation for metagenome
deseq2 metagenome mocat
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 10
2
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3
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2.1k
views
Using duplication rate as a covariate
deseq2 salmon fastp
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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1
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675
views
Dispersion shrinkage in DESeq2: LOESS instead of negative binomial based GLM?
deseq2 RNA-Seq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
4,840 results • Page 46 of 97
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Replies
Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
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.
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
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