Showing : RNA-SEQ • reset
40
votes
44
replies
9.2k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 5.8 years ago by ▴ 60 • written 6.4 years ago by ▴ 10
19
votes
11
replies
16k
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 7.6 years ago by 48k • written 7.6 years ago by ▴ 50
18
votes
12
replies
3.3k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 8.3 years ago by 40k • written 8.3 years ago by 7.8k
15
votes
12
replies
2.1k
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 5.1 years ago by 40k • written 5.1 years ago by ▴ 60
14
votes
9
replies
13k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
8.7 years ago gavrielmatt ▴ 30
14
votes
9
replies
3.3k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 5.7 years ago by ▴ 130 • written 7.4 years ago by ▴ 80
12
votes
2
replies
3.1k
views
How does edgeR compare to lme4?
rna-seq edger mixed model random effects lme4
updated 7.2 years ago by 48k • written 7.3 years ago by ▴ 80
11
votes
8
replies
7.7k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 7.0 years ago by ★ 2.8k • written 7.0 years ago by ▴ 70
10
votes
4
replies
3.8k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 7.2 years ago by 48k • written 7.2 years ago by ▴ 110
10
votes
9
replies
1.4k
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 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
10
votes
10
replies
5.2k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
5.5 years ago • updated 4.7 years ago rached ▴ 50
9
votes
11
replies
7.0k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 8.2 years ago by 48k • written 8.2 years ago by ▴ 30
9
votes
1
reply
3.0k
views
limma Time Course Experiment with many time points
limma RNA-Seq
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 130
9
votes
14
replies
7.7k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
7.2 years ago • updated 7.1 years ago anand_mt ▴ 80
9
votes
11
replies
5.2k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 6.6 years ago by ▴ 20 • written 7.4 years ago by ▴ 10
8
votes
3
replies
2.4k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 5.9 years ago by 40k • written 5.9 years ago by ▴ 50
8
votes
2
replies
5.6k
views
interpreting LRT results DESeq2
deseq2 LRT RNA-Seq
updated 8.5 years ago by 40k • written 8.5 years ago by ▴ 90
7
votes
7
replies
3.5k
views
Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
limma duplicateCorrelation rna-seq technical replicates biological replicates
updated 3.9 years ago by ★ 28k • written 4.0 years ago by ▴ 50
7
votes
7
replies
1.3k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 4.9 years ago by 21k • written 4.9 years ago by ▴ 50
7
votes
6
replies
762
views
Odd DESeq2 results - high significance in genes with too many zeros
deseq2 rna-seq
updated 3.2 years ago by 40k • written 3.2 years ago by • 0
6
votes
6
replies
863
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 3.6 years ago by 13k • written 3.6 years ago by • 0
6
votes
5
replies
1.7k
views
Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
limma rna-seq mixed model repeated measures
updated 5.0 years ago by 48k • written 5.0 years ago by ▴ 270
6
votes
5
replies
1.6k
views
How to know if I should use voomWithQualityWeights() or not?
limma RNA-Seq voom voomWithQualityWeights edgeR
updated 3.5 years ago by 48k • written 3.5 years ago by • 0
6
votes
7
replies
3.4k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq rna-seq linear model limma
updated 6.5 years ago by ★ 28k • written 6.5 years ago by ▴ 90
6
votes
1
reply
2.7k
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 7.0 years ago by 13k • written 7.0 years ago by ▴ 20
6
votes
4
replies
2.0k
views
Minimum number of samples per treatment/group for WGCNA analysis
WGCNA RNA-seq GCN gene coexpression network
updated 4.4 years ago by ▴ 20 • written 4.4 years ago by ▴ 40
5
votes
3
replies
2.7k
views
Understanding edgeR coefficients and design
edger r edger de rna-seq
updated 8.2 years ago by 48k • written 8.2 years ago by ▴ 30
5
votes
5
replies
4.7k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 4.5 years ago by 40k • written 4.5 years ago by ▴ 50
5
votes
5
replies
1.4k
views
Extract specific contrast from paired multifactor design matrix
edger deseq2 rna-seq
updated 8.2 years ago by 63k • written 8.2 years ago by ★ 2.0k
5
votes
2
replies
17k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 20 months ago by • 0 • written 4.7 years ago by ▴ 30
5
votes
7
replies
563
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 3 months ago by 48k • written 3 months ago by ▴ 10
5
votes
7
replies
1.7k
views
limma - blocking or regressing out nuisance variable
limma voom RNA-seq
updated 4.4 years ago by 63k • written 4.4 years ago by ▴ 20
5
votes
6
replies
1.3k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 3.0 years ago by 63k • written 3.0 years ago by ▴ 20
5
votes
4
replies
1.6k
views
RNA-seq Normalisation - normalise all samples in experiment or only the ones used in the comparison?
rna-seq normalization edgeR limma
updated 6.6 years ago by 48k • written 6.6 years ago by • 0
5
votes
4
replies
1.3k
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 6.1 years ago by ★ 28k • written 6.1 years ago by ▴ 10
5
votes
5
replies
1.2k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
19 months ago • updated 16 months ago 9906201a ▴ 20
5
votes
9
replies
1.2k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
14 months ago Yang Shi ▴ 10
5
votes
1
reply
845
views
DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
5
votes
5
replies
1.1k
views
edgeR no residual degrees of freedom for a specific row of numbers in dispCoxReidInterpolateTagwise
edger rna-seq
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 180
5
votes
3
replies
1.9k
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 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
5
votes
7
replies
2.4k
views
problem for Using RNA-seq data-set in WGCNA
WGCNA RNA-seq
updated 5.2 years ago by ★ 2.8k • written 5.2 years ago by ▴ 10
5
votes
11
replies
2.7k
views
DESeq2 logfoldchange and interaction in model
deseq2 R logfoldchange rna-seq
4.3 years ago • updated 4.2 years ago pierre.marin • 0
5
votes
3
replies
1.1k
views
Combining counts from non-replicate samples in RNA-Seq analysis for a synergistic system
edger normalization counts RNA-seq
updated 4.3 years ago by ★ 28k • written 4.3 years ago by • 0
5
votes
7
replies
1.3k
views
Co-expression between host and pathogen genes
edger rna-seq
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 10
5
votes
3
replies
977
views
DESeq2 with multiple treatments but no replicates
deseq2 rna-seq
updated 4.1 years ago by 40k • written 4.1 years ago by ▴ 20
5
votes
3
replies
2.7k
views
Error when calculating DE using the classical approach in edgeR
edgeR differential expression rna-seq
updated 7.0 years ago by 48k • written 7.0 years ago by • 0
5
votes
12
replies
4.7k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 23 months ago by ▴ 30 • written 6.0 years ago by ▴ 40
5
votes
2
replies
1.6k
views
DESeq2 batch effect with and without interaction model
deseq2 rna-seq R linear model design matrix
updated 5.8 years ago by 40k • written 5.8 years ago by ▴ 10
5
votes
6
replies
940
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 4.0 years ago by ▴ 810 • written 4.1 years ago by ▴ 10
4
votes
6
replies
3.0k
views
DESeq2 vst normalization: Do I have a heteroscedasticity problem and if so, what can I do about it?
deseq2 normalization rna-seq TCGA vst
updated 4.6 years ago by 40k • written 4.6 years ago by ▴ 70
50 results • Page 1 of 1
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Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Sorry for missing that one too. When writting blocks to an HDF5 file, the `write_block()` method for HDF5RealizationSink or TENxRealizatio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Hi Koki, sorry for not seeing this before. > will SparseArraySeed in DelayedArray be replaced by this new sparse array format? Yes it wil…
Comment: Manual creation of qPCRset does not work by Ed Siefker ▴ 230
Thanks! This works for me.
Answer: Manual creation of qPCRset does not work by James W. MacDonald 63k
``` > mat <- matrix(rnorm(6*96), ncol = 6, nrow = 96, byrow = FALSE) > pd <- new("AnnotatedDataFrame", data = data.frame(1:6, row.names …
Answer: ukb Chromosomal position information was converted into SNPS by James W. MacDonald 63k
In my work, we almost always convert RSIDs to chr:pos because the former is ambiguous and changing whereas the latter is not. Which is like…
Votes
Answer: Manual creation of qPCRset does not work
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
Answer: comparing contrasts in edger/lima using makeContrasts function
Awards • All
Popular Question to komal.rathi ▴ 110
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