Showing : RNA-Seq • reset
17
votes
11
replies
14k
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 6.3 years ago by 45k • written 6.3 years ago by ▴ 40
4
votes
3
replies
12k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 2.8 years ago by 45k • written 3.5 years ago by • 0
4
votes
8
replies
11k
views
Variance stabilising transformation for machine learning
deseq2 vst rna-seq machine-learning
updated 2.8 years ago by 37k • written 2.8 years ago by ▴ 20
11
votes
9
replies
10k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
7.4 years ago gavrielmatt ▴ 10
5
votes
2
replies
9.9k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 3 months ago by • 0 • written 3.4 years ago by ▴ 20
1
vote
14
replies
8.8k
views
DESeq Error in round(assay(se)) : non-numeric argument to mathematical function
deseq rna-seq
7.2 years ago rodriguez.varenka • 0
2
votes
6
replies
8.6k
views
DESeq2: QQ plot of P-values
deseq2 rnaseq rna-seq
4.8 years ago nikmehr22 • 0
40
votes
44
replies
7.3k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 4.4 years ago by ▴ 60 • written 5.0 years ago by ▴ 10
11
votes
8
replies
6.6k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 5.7 years ago by ★ 2.6k • written 5.7 years ago by ▴ 70
9
votes
14
replies
6.1k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
5.8 years ago • updated 5.7 years ago anand_mt ▴ 80
2
votes
10
replies
6.0k
views
adjusted p-values and p-values problems!
pvalue adjusted pvalue r bonferroni rna-seq
updated 5.6 years ago by 37k • written 5.6 years ago by ▴ 10
8
votes
11
replies
5.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 6.9 years ago by 45k • written 6.9 years ago by ▴ 20
3
votes
3
replies
5.2k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 7.2 years ago by ▴ 360 • written 7.2 years ago by • 0
4
votes
2
replies
4.8k
views
interpreting LRT results DESeq2
deseq2 LRT RNA-Seq
updated 7.2 years ago by 37k • written 7.2 years ago by ▴ 70
9
votes
11
replies
4.6k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 5.2 years ago by ▴ 20 • written 6.1 years ago by ▴ 10
4
votes
5
replies
4.6k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 6.0 years ago by ★ 3.4k • written 6.1 years ago by ▴ 180
1
vote
13
replies
4.5k
views
"Over-correction" in the size-factors of the DESeq2 package
deseq2 rna-seq normalization
6.1 years ago gil.hornung • 0
3
votes
7
replies
4.4k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 4.1 years ago by ▴ 20 • written 6.3 years ago by ▴ 40
3
votes
4
replies
4.4k
views
DESeq2 Time course analysis design - only time points WITHOUT treatments
rna-seq deseq2 multiple time points
updated 4.7 years ago by 37k • written 4.7 years ago by ▴ 10
0
votes
1
reply
4.2k
views
Subset data within DeSeq results object
deseq2 R rna-seq
updated 4.7 years ago by 37k • written 4.7 years ago by • 0
0
votes
2
replies
4.0k
views
PlotMA Filters for DeSEQ2 ; adjusting script
deseq2 rnaseq plotMA deseq rna-seq
updated 6.2 years ago by 37k • written 6.2 years ago by • 0
1
vote
5
replies
3.4k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 4.7 years ago by ★ 27k • written 4.7 years ago by ▴ 20
10
votes
10
replies
3.2k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
4.2 years ago • updated 3.3 years ago rached ▴ 50
1
vote
1
reply
3.1k
views
WGCNA - signedKME function
WGCNA RNA-seq signedKME
updated 7.4 years ago by ★ 2.6k • written 7.4 years ago by ▴ 10
5
votes
12
replies
3.1k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 6 months ago by ▴ 30 • written 4.6 years ago by ▴ 40
3
votes
7
replies
3.0k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 6.2 years ago by 45k • written 6.2 years ago by ▴ 70
10
votes
4
replies
2.9k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 5.8 years ago by 45k • written 5.8 years ago by ▴ 100
3
votes
6
replies
2.9k
views
edgeR: Error in taglist[[i]] : subscript out of bounds
edger rna-seq
updated 6.9 years ago by 45k • written 6.9 years ago by ▴ 60
1
vote
8
replies
2.8k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 17 months ago by 37k • written 2.5 years ago by • 0
4
votes
5
replies
2.8k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 4.0 years ago by 45k • written 4.0 years ago by ▴ 10
2
votes
3
replies
2.8k
views
Analysis of RNA-seq time series with edgeR
edger rna-seq differential expression timecourse time course
updated 5.6 years ago by ★ 27k • written 5.6 years ago by • 0
5
votes
5
replies
2.7k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 3.2 years ago by 37k • written 3.2 years ago by ▴ 50
3
votes
3
replies
2.6k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 4.8 years ago by 21k • written 4.8 years ago by ▴ 20
0
votes
2
replies
2.6k
views
WGCNA - problems picking a suitable power
WGCNA pickSoftThreshold power RNA-Seq
updated 6.3 years ago by ★ 2.6k • written 6.3 years ago by ▴ 10
14
votes
9
replies
2.6k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 4.3 years ago by ▴ 120 • written 6.1 years ago by ▴ 80
9
votes
1
reply
2.5k
views
limma Time Course Experiment with many time points
limma RNA-Seq
updated 6.6 years ago by ★ 27k • written 6.6 years ago by ▴ 130
1
vote
8
replies
2.5k
views
RNA-seq bacterial transcriptome analysis in EdgeR with unusual dispersion trend
RNA-seq edgeR estimatedispersions bacteria
7.3 years ago Mauve • 0
18
votes
12
replies
2.5k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 6.9 years ago by 37k • written 6.9 years ago by 7.8k
2
votes
1
reply
2.5k
views
voomWithQualityWeights, design and weights
voom limma-voom voomwithqualityweights rna-seq
updated 4.3 years ago by ▴ 1000 • written 4.3 years ago by ▴ 20
1
vote
5
replies
2.5k
views
WGCNA - How to prevent "blockwiseModules" command from dividing genes into multiple blocks?
WGCNA RNA-Seq
updated 5.6 years ago by ★ 2.6k • written 5.6 years ago by ▴ 70
3
votes
12
replies
2.4k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 3.7 years ago by ★ 2.6k • written 3.7 years ago by ▴ 10
12
votes
2
replies
2.4k
views
How does edgeR compare to lme4?
rna-seq edger mixed model random effects lme4
updated 5.9 years ago by 45k • written 5.9 years ago by ▴ 80
6
votes
7
replies
2.3k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq rna-seq linear model limma
updated 5.2 years ago by ★ 27k • written 5.2 years ago by ▴ 80
0
votes
1
reply
2.2k
views
Ballgown Error in file(file, "rt") : invalid 'description' argument
rna-seq ballgown
updated 4.7 years ago by ▴ 210 • written 4.7 years ago by • 0
3
votes
4
replies
2.2k
views
About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
4.7 years ago David Requena ▴ 20
4
votes
6
replies
2.2k
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 3.2 years ago by 37k • written 3.2 years ago by ▴ 70
0
votes
3
replies
2.1k
views
Normalisation - Deseq2 vs StingTie-Ballgown
deseq2 StringTie RNA-seq normalisation
updated 2.4 years ago by 37k • written 2.4 years ago by • 0
3
votes
4
replies
2.1k
views
Bioconductor vignette on Time course experiments only describes how to plot the the gene with the smallest p-value. How can I plot specific genes of …
timecourse time course rna-seq deseq2 ggplot2
6.7 years ago moldach ▴ 20
5
votes
3
replies
2.1k
views
Understanding edgeR coefficients and design
edger r edger de rna-seq
updated 6.9 years ago by 45k • written 6.9 years ago by ▴ 20
5
votes
3
replies
2.0k
views
Error when calculating DE using the classical approach in edgeR
edgeR differential expression rna-seq
updated 5.7 years ago by 45k • written 5.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: RPX PXDataset error by Laurent Gatto 1.5k
- From the URL in the error, it looks like you have the latest (or a recent) `rpx` version. It is generally recommended to add the output o…
Answer: Package name already exists due to previous issue by shepherl 3.1k
This has been resolved. There needed to be a manual intervention by the core team to remove the old issue from the issue tracker database.…
Answer: Package name already exists due to previous issue by James W. MacDonald 59k
You should probably send this question to bioc-devel@r-project.org
Comment: edgeR - how to convert DGELRT and other classes to .csv files by Benjamin • 0
Thank you Aaron. I am wondering if you know how to write the .csv file with both the topTags (statistical analysis) and the original counts…
Answer: error with: .make_splicings <- function(exons, cds, stop_codons=NULL) by James W. MacDonald 59k
That's a very old build, and an old version of the GFF standard. You would be better off getting something more recent. ``` > txdb <- m…
Votes
Comment: Merging two plated in R
Answer: Merging two plated in R
Answer: Merging two plated in R
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
A: Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
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