Showing : RNA-Seq • reset
17
votes
11
replies
13k
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 5.6 years ago by 43k • written 5.6 years ago by ▴ 40
9
votes
9
replies
9.2k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
6.7 years ago gavrielmatt • 0
1
vote
14
replies
8.3k
views
DESeq Error in round(assay(se)) : non-numeric argument to mathematical function
deseq rna-seq
6.5 years ago rodriguez.varenka • 0
4
votes
2
replies
6.6k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 2.7 years ago by ▴ 20
11
votes
8
replies
6.2k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 5.0 years ago by ★ 2.6k • written 5.0 years ago by ▴ 70
40
votes
44
replies
6.1k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 3.8 years ago by ▴ 60 • written 4.3 years ago by ▴ 10
9
votes
14
replies
5.4k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
5.1 years ago anand_mt ▴ 80
8
votes
11
replies
5.2k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 20
2
votes
10
replies
5.0k
views
adjusted p-values and p-values problems!
pvalue adjusted pvalue r bonferroni rna-seq
updated 5.0 years ago by 34k • written 5.0 years ago by ▴ 10
3
votes
3
replies
4.7k
views
Find DEG from RNA-seq: What if have only RPKM data?
deg rna-seq rpkm
updated 6.5 years ago by ▴ 340 • written 6.5 years ago by • 0
4
votes
2
replies
4.5k
views
interpreting LRT results DESeq2
deseq2 LRT RNA-Seq
updated 6.5 years ago by 34k • written 6.5 years ago by ▴ 70
4
votes
3
replies
4.4k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 2.2 years ago by 43k • written 2.8 years ago by • 0
9
votes
11
replies
4.1k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 4.6 years ago by ▴ 20 • written 5.4 years ago by ▴ 10
4
votes
5
replies
4.1k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 5.3 years ago by ★ 3.3k • written 5.4 years ago by ▴ 180
1
vote
13
replies
4.1k
views
"Over-correction" in the size-factors of the DESeq2 package
deseq2 rna-seq normalization
5.4 years ago gil.hornung • 0
3
votes
7
replies
4.1k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 3.5 years ago by ▴ 20 • written 5.6 years ago by ▴ 40
3
votes
4
replies
4.0k
views
DESeq2 Time course analysis design - only time points WITHOUT treatments
rna-seq deseq2 multiple time points
updated 4.1 years ago by 34k • written 4.1 years ago by ▴ 10
2
votes
8
replies
3.8k
views
Variance stabilising transformation for machine learning
deseq2 vst rna-seq machine-learning
updated 2.1 years ago by 34k • written 2.1 years ago by • 0
0
votes
2
replies
3.7k
views
PlotMA Filters for DeSEQ2 ; adjusting script
deseq2 rnaseq plotMA deseq rna-seq
updated 5.5 years ago by 34k • written 5.5 years ago by • 0
0
votes
1
reply
3.4k
views
Subset data within DeSeq results object
deseq2 R rna-seq
updated 4.1 years ago by 34k • written 4.1 years ago by • 0
1
vote
1
reply
3.0k
views
WGCNA - signedKME function
WGCNA RNA-seq signedKME
updated 6.7 years ago by ★ 2.6k • written 6.7 years ago by ▴ 10
1
vote
5
replies
2.7k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 4.0 years ago by ★ 27k • written 4.0 years ago by ▴ 20
3
votes
7
replies
2.7k
views
edgeR glmLRT and interaction effect: an example
rna-seq edger glmlrt interactions
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 70
3
votes
6
replies
2.7k
views
edgeR: Error in taglist[[i]] : subscript out of bounds
edger rna-seq
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 60
2
votes
6
replies
2.6k
views
DESeq2: QQ plot of P-values
deseq2 rnaseq rna-seq
4.1 years ago nikmehr22 • 0
10
votes
4
replies
2.5k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 90
2
votes
3
replies
2.5k
views
Analysis of RNA-seq time series with edgeR
edger rna-seq differential expression timecourse time course
updated 4.9 years ago by ★ 27k • written 4.9 years ago by • 0
5
votes
11
replies
2.5k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 5 months ago by • 0 • written 4.0 years ago by ▴ 40
0
votes
2
replies
2.3k
views
WGCNA - problems picking a suitable power
WGCNA pickSoftThreshold power RNA-Seq
updated 5.6 years ago by ★ 2.6k • written 5.6 years ago by ▴ 10
1
vote
8
replies
2.3k
views
RNA-seq bacterial transcriptome analysis in EdgeR with unusual dispersion trend
RNA-seq edgeR estimatedispersions bacteria
6.6 years ago Mauve • 0
9
votes
1
reply
2.3k
views
limma Time Course Experiment with many time points
limma RNA-Seq
updated 5.9 years ago by ★ 27k • written 5.9 years ago by ▴ 130
14
votes
9
replies
2.3k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 3.7 years ago by ▴ 110 • written 5.4 years ago by ▴ 70
3
votes
3
replies
2.2k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 4.1 years ago by 21k • written 4.1 years ago by ▴ 20
10
votes
10
replies
2.2k
views
Pre-processing RNA-seq data (normalization and transformation) for GSVA
gsva gene set variation analysis normalization transformation rna-seq
3.5 years ago • updated 2.7 years ago rached ▴ 50
18
votes
12
replies
2.2k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 6.3 years ago by 34k • written 6.3 years ago by 7.6k
1
vote
5
replies
2.2k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
12
votes
2
replies
2.2k
views
How does edgeR compare to lme4?
rna-seq edger mixed model random effects lme4
updated 5.2 years ago by 43k • written 5.2 years ago by ▴ 70
0
votes
1
reply
2.0k
views
Ballgown Error in file(file, "rt") : invalid 'description' argument
rna-seq ballgown
updated 4.0 years ago by ▴ 210 • written 4.0 years ago by • 0
1
vote
1
reply
2.0k
views
voomWithQualityWeights, design and weights
voom limma-voom voomwithqualityweights rna-seq
updated 3.6 years ago by ▴ 1000 • written 3.6 years ago by ▴ 10
1
vote
5
replies
2.0k
views
WGCNA - How to prevent "blockwiseModules" command from dividing genes into multiple blocks?
WGCNA RNA-Seq
updated 5.0 years ago by ★ 2.6k • written 5.0 years ago by ▴ 70
6
votes
7
replies
2.0k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq rna-seq linear model limma
updated 4.5 years ago by ★ 27k • written 4.5 years ago by ▴ 80
3
votes
12
replies
2.0k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 3.0 years ago by ★ 2.6k • written 3.0 years ago by ▴ 10
5
votes
5
replies
1.9k
views
Differential Expression Analysis between conditions of single cell RNA-Seq
deseq2 scRNA-Seq RNA-Seq differential expression analysis
updated 2.5 years ago by 34k • written 2.5 years ago by ▴ 50
3
votes
4
replies
1.9k
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
6.0 years ago moldach ▴ 20
5
votes
3
replies
1.9k
views
Understanding edgeR coefficients and design
edger r edger de rna-seq
updated 6.2 years ago by 43k • written 6.2 years ago by ▴ 20
0
votes
1
reply
1.8k
views
how to infer missing PAM50 molecular subtypes in TCGA-BRCA dataset downloaded with TCGABiolinks?
tcgabiolinks tcga-brca gdc pam50 rna-seq
3.5 years ago pfrancislyon • 0
0
votes
2
replies
1.8k
views
DESeq2 different results from similar datasets
deseq2 differential gene expression rna-seq
5.8 years ago erin.gill81 ▴ 50
4
votes
6
replies
1.8k
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 2.6 years ago by 34k • written 2.6 years ago by ▴ 70
1
vote
2
replies
1.8k
views
Deconvolution RNA-Seq data
rna-seq differential expression
updated 6.6 years ago by 58k • written 6.6 years ago by ▴ 10
0
votes
2
replies
1.7k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
5.7 years ago hywel.williams • 0
50 results • Page 1 of 1
Recent ...
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Answer: Undefined columns error R cytometry analysis by Jiang, Mike ★ 1.3k
I see you are trying to fill the missing transform info to `gs_bcell_auto` , which is a hack, but since you seems to know what you are doin…
Comment: how to get MFI stats from data by Jiang, Mike ★ 1.3k
Can you grant the public caccess to you fcs to reproduce your issue?
Answer: Getting a dataset that only contains the flow data within the gated area by Jiang, Mike ★ 1.3k
You didn't post your example code, so here is my best guess of your workflow > library(flowCore) > library(flowWorkspace) …
Comment: Diffbind dba.plotProfile attempt to select less than one element in OneIndex by bhanratt • 0
``` > DBA 10 Samples, 31953 sites in matrix: ID Tissue Factor Condition Replicate Reads FRiP 1 58 1 H3K4me3 AD …
Answer: Warning messages on Apple M1 BigSur by Vincent J. Carey, Jr. 6.5k
We are not producing M1 binaries at this time. If you use the intel version of R under Rosetta 2 you can use the intel mac binaries.
Votes
Comment: Use of coef() as a measure of effect size in a multiple regression using DESeq2
Answer: Log fold change interpretation of time series with Wald test
A: gviz: name of tracks disappeas
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
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