Showing : RNA-SEQ • reset
41
votes
44
replies
11k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 6.8 years ago by ▴ 60 • written 7.3 years ago by ▴ 10
24
votes
11
replies
19k
views
when to apply quantile normalization with voom in limma/voom framework with RNA-seq data?
limma voom limma voom rna-seq quantile normalization
updated 8.6 years ago by 51k • written 8.6 years ago by ▴ 50
18
votes
12
replies
4.0k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 9.3 years ago by 42k • written 9.3 years ago by ★ 7.9k
15
votes
12
replies
2.7k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2 ZINB-WaVE single cell RNA-seq differential expression
updated 6.1 years ago by 42k • written 6.1 years ago by ▴ 60
14
votes
9
replies
4.0k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 6.6 years ago by ▴ 130 • written 8.4 years ago by ▴ 80
14
votes
9
replies
16k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
9.7 years ago gavrielmatt ▴ 30
12
votes
10
replies
7.3k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
6.5 years ago • updated 5.7 years ago rached ▴ 60
12
votes
2
replies
3.7k
views
How does edgeR compare to lme4?
rna-seq edger mixed model random effects lme4
updated 8.2 years ago by 51k • written 8.2 years ago by ▴ 80
11
votes
8
replies
9.2k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 8.0 years ago by ★ 3.0k • written 8.0 years ago by ▴ 70
11
votes
3
replies
3.4k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 6.9 years ago by 42k • written 6.9 years ago by ▴ 60
10
votes
4
replies
4.7k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 8.1 years ago by 51k • written 8.1 years ago by ▴ 110
10
votes
14
replies
9.0k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
8.1 years ago anand_mt ▴ 90
10
votes
9
replies
1.9k
views
Is there are better way to improve the design via blocking or contrasts while using limma-voom for the mentioned datasets?
limma-voom voom limma rna-seq
updated 6.9 years ago by ★ 28k • written 6.9 years ago by • 0
9
votes
12
replies
8.3k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 5 months ago by • 0 • written 9.2 years ago by ▴ 30
9
votes
11
replies
5.8k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 7.6 years ago by ▴ 20 • written 8.4 years ago by ▴ 10
9
votes
1
reply
3.3k
views
limma Time Course Experiment with many time points
limma RNA-Seq
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 130
8
votes
5
replies
3.0k
views
How to know if I should use voomWithQualityWeights() or not?
limma RNA-Seq voom voomWithQualityWeights edgeR
updated 4.5 years ago by 51k • written 4.5 years ago by ▴ 10
8
votes
7
replies
5.6k
views
Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
limma duplicateCorrelation rna-seq technical replicates biological replicates
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 50
8
votes
2
replies
6.2k
views
interpreting LRT results DESeq2
deseq2 LRT RNA-Seq
updated 9.5 years ago by 42k • written 9.5 years ago by ▴ 90
7
votes
6
replies
1.2k
views
Odd DESeq2 results - high significance in genes with too many zeros
deseq2 rna-seq
updated 4.2 years ago by 42k • written 4.2 years ago by • 0
7
votes
7
replies
1.8k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 5.9 years ago by 21k • written 5.9 years ago by ▴ 50
7
votes
1
reply
3.6k
views
Using R package 'limma' on pre-normalized counts and the effect of non-equivalent reads/sample on limma linear model
limma rna-seq multi-mapped reads normalization microbiome
updated 8.0 years ago by ★ 13k • written 8.0 years ago by ▴ 20
7
votes
4
replies
3.2k
views
Minimum number of samples per treatment/group for WGCNA analysis
WGCNA RNA-seq GCN gene coexpression network
updated 5.3 years ago by ▴ 20 • written 5.4 years ago by ▴ 50
6
votes
6
replies
1.3k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 4.6 years ago by ★ 13k • written 4.6 years ago by • 0
6
votes
5
replies
2.4k
views
Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
limma rna-seq mixed model repeated measures
updated 6.0 years ago by 51k • written 6.0 years ago by ▴ 280
6
votes
7
replies
4.3k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq rna-seq linear model limma
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 90
6
votes
6
replies
6.6k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 23 months ago by ▴ 200 • written 6.3 years ago by ▴ 10
5
votes
2
replies
24k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.7 years ago by ▴ 30
5
votes
3
replies
3.3k
views
Understanding edgeR coefficients and design
edger r edger de rna-seq
updated 9.2 years ago by 51k • written 9.2 years ago by ▴ 30
5
votes
5
replies
1.7k
views
Extract specific contrast from paired multifactor design matrix
edger deseq2 rna-seq
updated 9.2 years ago by 67k • written 9.2 years ago by ★ 2.1k
5
votes
5
replies
6.6k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 5.5 years ago by 42k • written 5.5 years ago by ▴ 60
5
votes
4
replies
2.2k
views
RNA-seq Normalisation - normalise all samples in experiment or only the ones used in the comparison?
rna-seq normalization edgeR limma
updated 7.6 years ago by 51k • written 7.6 years ago by • 0
5
votes
4
replies
1.7k
views
Testing for DE genes between samples of isolated cells, accounting for expression in whole tissue
limma rnaseq rna-seq model-matrix multiple factor design
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 10
5
votes
2
replies
1.6k
views
Correct usage of tximport counts in edgeR without offset matrix.
tximport edgeR rna-seq
updated 5.8 years ago by 67k • written 5.8 years ago by • 0
5
votes
6
replies
1.5k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 5.0 years ago by ▴ 860 • written 5.0 years ago by ▴ 10
5
votes
3
replies
2.3k
views
Correct contrast for testing multi-level interaction effect in limma using combined factors design matrix
limma contrast matrix limma design matrix limma rna-seq limma voom
updated 7.4 years ago by ★ 28k • written 7.4 years ago by • 0
5
votes
11
replies
3.6k
views
DESeq2 logfoldchange and interaction in model
deseq2 R logfoldchange rna-seq
5.3 years ago • updated 5.2 years ago pierre.marin • 0
5
votes
7
replies
3.0k
views
problem for Using RNA-seq data-set in WGCNA
WGCNA RNA-seq
updated 6.2 years ago by ★ 3.0k • written 6.2 years ago by ▴ 10
5
votes
1
reply
1.1k
views
DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
5
votes
5
replies
1.5k
views
edgeR no residual degrees of freedom for a specific row of numbers in dispCoxReidInterpolateTagwise
edger rna-seq
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 180
5
votes
7
replies
3.8k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 6.0 years ago by 42k • written 6.0 years ago by ▴ 10
5
votes
3
replies
1.5k
views
Combining counts from non-replicate samples in RNA-Seq analysis for a synergistic system
edger normalization counts RNA-seq
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
5
votes
2
replies
2.1k
views
DESeq2 batch effect with and without interaction model
deseq2 rna-seq R linear model design matrix
updated 6.8 years ago by 42k • written 6.8 years ago by ▴ 10
5
votes
3
replies
3.3k
views
Error when calculating DE using the classical approach in edgeR
edgeR differential expression rna-seq
updated 8.0 years ago by 51k • written 8.0 years ago by • 0
5
votes
7
replies
2.5k
views
limma - blocking or regressing out nuisance variable
limma voom RNA-seq
updated 5.4 years ago by 67k • written 5.4 years ago by ▴ 20
5
votes
7
replies
1.6k
views
Co-expression between host and pathogen genes
edger rna-seq
updated 8.4 years ago by ★ 28k • written 8.5 years ago by ▴ 10
5
votes
3
replies
2.8k
views
Analyzing RNA-seq data by WGCNA
wgcna rna-seq
updated 8.0 years ago by ★ 3.0k • written 8.0 years ago by ▴ 20
5
votes
12
replies
5.9k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 2.9 years ago by ▴ 30 • written 7.0 years ago by ▴ 40
5
votes
3
replies
1.3k
views
DESeq2 with multiple treatments but no replicates
deseq2 rna-seq
updated 5.1 years ago by 42k • written 5.1 years ago by ▴ 20
5
votes
6
replies
1.8k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 4.0 years ago by 67k • written 4.0 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: How to read OSCA book? by zr • 0
Got it, that had really confused me a bit, thank you for your help!
Comment: How to use removeBatchEffect for removing effect of multiple confounding variabl by James W. MacDonald 67k
Please don't add questions onto a four-year old post. Instead, start a new one. If you want to reference the old post, that's fine.
Answer: How to use removeBatchEffect for removing effect of multiple confounding variabl by bioinformata • 0
Is it feasible to remove batch effect with limma after variance stabilizing transformation of the gene expression , or is eough to use vst…
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by James W. MacDonald 67k
Hi Guido, It's that last filtering step. You are saying the NCBI Gene ID has to be unique AND the ontology has to be BP, which isn't what …
Comment: AffylmGUI does not start wit R 4.4.1 by richardallenfriedmanbrooklyn ▴ 20
Gordon, I found out what went wrong. The problem was that the xquartz distribution for mac from cran did not include tcltk! I found that b…
Votes
Answer: How to read OSCA book?
Answer: How to read OSCA book?
DESeq2 design and contrasts with 2 drug-treated and one control group
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
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