Showing : RNA-seq • reset
41
votes
44
replies
12k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 7.1 years ago by ▴ 60 • written 7.7 years ago by ▴ 10
24
votes
11
replies
20k
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 9.0 years ago by 52k • written 9.0 years ago by ▴ 50
18
votes
12
replies
4.2k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 9.6 years ago by 43k • written 9.6 years ago by ★ 7.9k
15
votes
12
replies
2.9k
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 6.4 years ago by 43k • written 6.4 years ago by ▴ 60
14
votes
9
replies
17k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
10.0 years ago gavrielmatt ▴ 30
14
votes
9
replies
4.2k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 7.0 years ago by ▴ 130 • written 8.7 years ago by ▴ 80
12
votes
10
replies
7.9k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
6.8 years ago • updated 6.0 years ago rached ▴ 60
12
votes
2
replies
3.9k
views
How does edgeR compare to lme4?
rna-seq edger mixed model random effects lme4
updated 8.6 years ago by 52k • written 8.6 years ago by ▴ 80
11
votes
3
replies
3.7k
views
Testing three-way interactions in DESeq2
deseq2 rna-seq rnaseq interactions
updated 7.3 years ago by 43k • written 7.3 years ago by ▴ 60
11
votes
8
replies
10.0k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 8.3 years ago by ★ 3.0k • written 8.3 years ago by ▴ 70
10
votes
14
replies
9.3k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
8.5 years ago • updated 8.4 years ago anand_mt ▴ 90
10
votes
4
replies
5.0k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 8.5 years ago by 52k • written 8.5 years ago by ▴ 110
10
votes
9
replies
2.1k
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 7.2 years ago by ★ 28k • written 7.2 years ago by • 0
9
votes
12
replies
8.6k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 9 months ago by • 0 • written 9.5 years ago by ▴ 30
9
votes
11
replies
5.9k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 7.9 years ago by ▴ 20 • written 8.7 years ago by ▴ 10
9
votes
1
reply
3.4k
views
limma Time Course Experiment with many time points
limma RNA-Seq
updated 9.2 years ago by ★ 28k • written 9.2 years ago by ▴ 130
8
votes
5
replies
3.4k
views
How to know if I should use voomWithQualityWeights() or not?
limma RNA-Seq voom voomWithQualityWeights edgeR
updated 4.8 years ago by 52k • written 4.8 years ago by ▴ 10
8
votes
7
replies
6.4k
views
Further clarification on when not to use duplicateCorrelation with technical replicates (RNA-seq)
limma duplicateCorrelation rna-seq technical replicates biological replicates
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 50
8
votes
1
reply
3.9k
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 8.3 years ago by ★ 13k • written 8.3 years ago by ▴ 30
8
votes
2
replies
6.3k
views
interpreting LRT results DESeq2
deseq2 LRT RNA-Seq
updated 9.8 years ago by 43k • written 9.8 years ago by ▴ 90
7
votes
6
replies
1.3k
views
Odd DESeq2 results - high significance in genes with too many zeros
deseq2 rna-seq
updated 4.5 years ago by 43k • written 4.5 years ago by • 0
7
votes
7
replies
1.9k
views
Using GenomicDataCommons R package to identify cases with both DNA methylation and gene expression data
R gdc rna-seq dna methylation
updated 6.2 years ago by 21k • written 6.2 years ago by ▴ 50
7
votes
4
replies
3.7k
views
Minimum number of samples per treatment/group for WGCNA analysis
WGCNA RNA-seq GCN gene coexpression network
updated 5.7 years ago by ▴ 20 • written 5.7 years ago by ▴ 50
6
votes
6
replies
1.5k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 4.9 years ago by ★ 13k • written 4.9 years ago by • 0
6
votes
4
replies
2.4k
views
RNA-seq Normalisation - normalise all samples in experiment or only the ones used in the comparison?
rna-seq normalization edgeR limma
updated 7.9 years ago by 52k • written 7.9 years ago by • 0
6
votes
5
replies
2.6k
views
Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
limma rna-seq mixed model repeated measures
updated 6.3 years ago by 52k • written 6.3 years ago by ▴ 280
6
votes
7
replies
4.6k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq rna-seq linear model limma
updated 7.9 years ago by ★ 28k • written 7.9 years ago by ▴ 90
6
votes
6
replies
7.0k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 2.3 years ago by ▴ 200 • written 6.7 years ago by ▴ 10
5
votes
2
replies
26k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.0 years ago by ▴ 30
5
votes
3
replies
3.5k
views
Understanding edgeR coefficients and design
edger r edger de rna-seq
updated 9.5 years ago by 52k • written 9.5 years ago by ▴ 30
5
votes
5
replies
1.8k
views
Extract specific contrast from paired multifactor design matrix
edger deseq2 rna-seq
updated 9.5 years ago by 67k • written 9.5 years ago by ★ 2.1k
5
votes
5
replies
7.2k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 5.9 years ago by 43k • written 5.9 years ago by ▴ 60
5
votes
4
replies
1.8k
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 7.4 years ago by ★ 28k • written 7.4 years ago by ▴ 10
5
votes
2
replies
1.8k
views
Correct usage of tximport counts in edgeR without offset matrix.
tximport edgeR rna-seq
updated 6.1 years ago by 67k • written 6.1 years ago by • 0
5
votes
6
replies
1.6k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 5.4 years ago by ▴ 900 • written 5.4 years ago by ▴ 10
5
votes
3
replies
2.5k
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 7.8 years ago by ★ 28k • written 7.8 years ago by • 0
5
votes
11
replies
3.9k
views
DESeq2 logfoldchange and interaction in model
deseq2 R logfoldchange rna-seq
5.6 years ago • updated 5.5 years ago pierre.marin • 0
5
votes
7
replies
3.1k
views
problem for Using RNA-seq data-set in WGCNA
WGCNA RNA-seq
updated 6.6 years ago by ★ 3.0k • written 6.6 years ago by ▴ 10
5
votes
1
reply
1.2k
views
DE analysis when large portion of transcriptome is changed
rna-seq edger ebseq differential expression
updated 6.5 years ago by ★ 28k • written 6.5 years ago by • 0
5
votes
5
replies
1.6k
views
edgeR no residual degrees of freedom for a specific row of numbers in dispCoxReidInterpolateTagwise
edger rna-seq
updated 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 180
5
votes
7
replies
4.0k
views
Deseq2 design for one condition over 8 different time point
deseq2 rna-seq design matrix deseq
updated 6.3 years ago by 43k • written 6.3 years ago by ▴ 10
5
votes
3
replies
1.6k
views
Combining counts from non-replicate samples in RNA-Seq analysis for a synergistic system
edger normalization counts RNA-seq
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
5
votes
2
replies
2.2k
views
DESeq2 batch effect with and without interaction model
deseq2 rna-seq R linear model design matrix
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 10
5
votes
3
replies
3.5k
views
Error when calculating DE using the classical approach in edgeR
edgeR differential expression rna-seq
updated 8.4 years ago by 52k • written 8.4 years ago by • 0
5
votes
7
replies
2.8k
views
limma - blocking or regressing out nuisance variable
limma voom RNA-seq
updated 5.7 years ago by 67k • written 5.7 years ago by ▴ 20
5
votes
7
replies
1.7k
views
Co-expression between host and pathogen genes
edger rna-seq
updated 8.8 years ago by ★ 28k • written 8.8 years ago by ▴ 10
5
votes
3
replies
3.0k
views
Analyzing RNA-seq data by WGCNA
wgcna rna-seq
updated 8.3 years ago by ★ 3.0k • written 8.3 years ago by ▴ 20
5
votes
12
replies
6.2k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 3.2 years ago by ▴ 30 • written 7.3 years ago by ▴ 40
5
votes
3
replies
1.4k
views
DESeq2 with multiple treatments but no replicates
deseq2 rna-seq
updated 5.4 years ago by 43k • written 5.4 years ago by ▴ 20
5
votes
6
replies
2.0k
views
RUVseq to remove a library size artefact in a zebrafish brain RNA-seq dataset
RUVSeq RUV RNA-seq
updated 4.3 years ago by 67k • written 4.3 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Answer: promoters_txdb <- promoters(txdb, upstream = 2000) is not 2000 by James W. MacDonald 67k
If you use `promoters` and do not provide an argument for something that has a default, you will get the default argument. Your last call t…
Comment: org.Hs.eg.db issue by k.panov • 0
installed R on another PC, works perfectly. ergo, problem outside of R probably..... :-(
Comment: MBDseq analysis using qsea package by Lukas ▴ 20
Hi, I checked in with Matthias and here is his response: You need to indicate "samples": "The indices of the samples for which individu…
Comment: DESeq2 analysis with transcript counts by sindhuri • 0
Thank you for the response. Currently I am using the R studio for analysis and Im running DESeq2 for analysis of the **transcript counts.ts…
Comment: iam not able to do retrive data using GEOquery R package by James W. MacDonald 67k
Another alternative is to use the `GEOmetadb` package ([vignette here)][1], which will allow you to make queries to identify GEO datasets t…
Votes
Answer: Issue carrying out DiffBind Analysis at a predefined peak set
Answer: Differential variability modelling with vst() expression
Answer: Differential variability modelling with vst() expression
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
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