Showing : RNA-Seq • reset
1
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14
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DESeq Error in round(assay(se)) : non-numeric argument to mathematical function
deseq rna-seq
10.1 years ago rodriguez.varenka • 0
0
votes
6
replies
1.9k
views
Which sequencing parameters are required for SGSeq analysis of splice events?
rna-seq alternative splicing SGSeq
6.5 years ago andrea.bast • 0
41
votes
44
replies
13k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 7.4 years ago by ▴ 60 • written 8.0 years ago by ▴ 10
3
votes
7
replies
6.3k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 7.1 years ago by ▴ 30 • written 9.2 years ago by ▴ 40
1
vote
3
replies
2.8k
views
Gene Ontology and Gene Set Enrichment
rna-seq bioinformatics gene ontology gene set enrichment go
updated 8.6 years ago by ★ 1.2k • written 8.6 years ago by ▴ 10
1
vote
4
replies
2.8k
views
strange FDR distribution for RNA-seq sample with edgeR
edgeR RNA-seq FDR
updated 10.4 years ago by 52k • written 10.4 years ago by ▴ 10
14
votes
9
replies
17k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
10.3 years ago gavrielmatt ▴ 30
2
votes
3
replies
4.3k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 19 months ago by 52k • written 19 months ago by • 0
3
votes
3
replies
2.1k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 8.2 years ago by 16k • written 8.2 years ago by ▴ 10
0
votes
3
replies
1.1k
views
3x2 comparisons in DEseq - time (3 time points) and two treatments
deseq2 deseq rna-seq multiple comparisons
updated 6.8 years ago by 43k • written 6.8 years ago by ▴ 60
0
votes
3
replies
2.2k
views
Redundant meta-features (genes) using FeatureCounts
rna-seq featurecounts
10.3 years ago ccheung • 0
0
votes
3
replies
1.3k
views
Analyzing a subgroups of samples, which result should I trust
deseq2 rna-seq
written 7.0 years ago by ▴ 20
9
votes
12
replies
8.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 12 months ago by • 0 • written 9.8 years ago by ▴ 30
3
votes
12
replies
6.7k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 6.6 years ago by ★ 3.0k • written 6.6 years ago by ▴ 10
0
votes
3
replies
4.2k
views
Handling pseudogenes in RNA-seq
rna-seq pseudogenes STAR counts
updated 6.9 years ago by ★ 1.1k • written 6.9 years ago by • 0
3
votes
3
replies
2.5k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 6.2 years ago by ★ 3.0k • written 6.2 years ago by ▴ 60
3
votes
6
replies
2.5k
views
DESeq2 with contaminating cell types
deseq2 rna-seq
updated 8.3 years ago by 43k • written 8.3 years ago by ▴ 100
2
votes
5
replies
2.0k
views
Differential Gene Expression
deseq2 bioinformatics rna-seq Tutorial
updated 8.6 years ago by 43k • written 8.6 years ago by ▴ 10
0
votes
3
replies
2.5k
views
How to set the contrast in case of a design of 2 level factor and interaction term.
deseq2 deseq rna-seq
10.4 years ago solgakar@bi.technion.ac.il ▴ 90
4
votes
4
replies
1.8k
views
Correlation analysis taking into account multiple correlations
edger rna-seq correlation
updated 8.6 years ago by ▴ 280 • written 8.6 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 9.3 years ago by 52k • written 9.3 years ago by ▴ 50
3
votes
3
replies
7.1k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 7.7 years ago by 21k • written 7.7 years ago by ▴ 20
3
votes
4
replies
5.7k
views
About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
7.6 years ago David Requena ▴ 20
2
votes
2
replies
2.3k
views
Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
tximport limma rna-seq
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 60
18
votes
12
replies
4.4k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 9.9 years ago by 43k • written 9.9 years ago by ★ 7.9k
3
votes
6
replies
4.3k
views
edgeR: Error in taglist[[i]] : subscript out of bounds
edger rna-seq
updated 9.8 years ago by 52k • written 9.8 years ago by ▴ 60
12
votes
2
replies
4.0k
views
How does edgeR compare to lme4?
rna-seq edger mixed model random effects lme4
updated 8.9 years ago by 52k • written 8.9 years ago by ▴ 80
1
vote
8
replies
3.6k
views
RNA-seq bacterial transcriptome analysis in EdgeR with unusual dispersion trend
RNA-seq edgeR estimatedispersions bacteria
10.2 years ago Mauve • 0
5
votes
3
replies
3.7k
views
Understanding edgeR coefficients and design
edger r edger de rna-seq
updated 9.8 years ago by 52k • written 9.8 years ago by ▴ 30
6
votes
5
replies
2.8k
views
Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
limma rna-seq mixed model repeated measures
updated 6.6 years ago by 52k • written 6.6 years ago by ▴ 280
1
vote
3
replies
3.0k
views
DESeq normalization seems to reverse the directionality of log2FoldChange - is this normal?
deseq2 rnaseq rna-seq normalization cpm
updated 9.0 years ago by ★ 13k • written 9.0 years ago by • 0
10
votes
14
replies
9.7k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
8.8 years ago • updated 8.7 years ago anand_mt ▴ 90
1
vote
13
replies
7.1k
views
"Over-correction" in the size-factors of the DESeq2 package
deseq2 rna-seq normalization
9.1 years ago gil.hornung • 0
3
votes
3
replies
1.4k
views
RNA-seq genes differentially expressed in combined treatment
DESeq2 deseq2 RNA-seq
9.1 years ago david.ashbrook • 0
0
votes
2
replies
3.2k
views
DESeq2 different results from similar datasets
deseq2 differential gene expression rna-seq
9.4 years ago erin.gill81 ▴ 60
4
votes
5
replies
6.7k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 8.9 years ago by ★ 3.6k • written 9.0 years ago by ▴ 180
4
votes
2
replies
2.9k
views
Quality control on RNA-Seq (level 3) data from TCGA
rna-seq GC-Content qualitycontrol
updated 9.5 years ago by ▴ 180 • written 9.5 years ago by ▴ 60
0
votes
3
replies
1.9k
views
Trouble with Custom PC Plot
deseq2 plotPCA PCA rna-seq
8.9 years ago newsomew13 • 0
9
votes
11
replies
6.1k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 8.2 years ago by ▴ 20 • written 9.0 years ago by ▴ 10
5
votes
7
replies
1.8k
views
Co-expression between host and pathogen genes
edger rna-seq
updated 9.1 years ago by ★ 28k • written 9.1 years ago by ▴ 10
0
votes
2
replies
3.1k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
9.3 years ago hywel.williams • 0
11
votes
8
replies
11k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 8.6 years ago by ★ 3.0k • written 8.6 years ago by ▴ 70
3
votes
4
replies
3.1k
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
9.6 years ago moldach ▴ 20
0
votes
4
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2.5k
views
Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
8.3 years ago bioinf ▴ 10
0
votes
2
replies
5.2k
views
PlotMA Filters for DeSEQ2 ; adjusting script
deseq2 rnaseq plotMA deseq rna-seq
updated 9.1 years ago by 43k • written 9.1 years ago by • 0
14
votes
9
replies
4.4k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 7.3 years ago by ▴ 130 • written 9.0 years ago by ▴ 80
10
votes
4
replies
5.3k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 8.8 years ago by 52k • written 8.8 years ago by ▴ 110
0
votes
2
replies
5.5k
views
WGCNA - problems picking a suitable power
WGCNA pickSoftThreshold power RNA-Seq
updated 9.2 years ago by ★ 3.0k • written 9.2 years ago by ▴ 10
2
votes
10
replies
2.5k
views
Design matrix for unbalanced data
edgeR RNA-Seq design matrix multifactorial design
9.2 years ago Yogender Gowtham ▴ 20
3
votes
2
replies
1.7k
views
Bayesian Network analysis of gene regulatory relationship
Bayesian network RNA-seq Gene regulatory network
7.6 years ago nancydong20 ▴ 10
50 results • Page 1 of 1
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Replies
Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2 by Tom • 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq by caroline.zanchi • 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Votes
Comment: Filtering after DESeq
A: Normalized counts from DESeq2 results in similar but not equal total read count?
A: DESeq2: Different Dispersions for different sample groups
A: Contrasts & coefficients in limma
Answer: How to formulate 2 factor nested design in DESeq2
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