Showing : RNA-seq • reset
1
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14
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11k
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DESeq Error in round(assay(se)) : non-numeric argument to mathematical function
deseq rna-seq
9.7 years ago rodriguez.varenka • 0
0
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6
replies
1.7k
views
Which sequencing parameters are required for SGSeq analysis of splice events?
rna-seq alternative splicing SGSeq
6.1 years ago andrea.bast • 0
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 7.0 years ago by ▴ 60 • written 7.6 years ago by ▴ 10
3
votes
7
replies
6.0k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 6.7 years ago by ▴ 30 • written 8.8 years ago by ▴ 40
1
vote
3
replies
2.5k
views
Gene Ontology and Gene Set Enrichment
rna-seq bioinformatics gene ontology gene set enrichment go
updated 8.2 years ago by ★ 1.2k • written 8.2 years ago by ▴ 10
1
vote
4
replies
2.7k
views
strange FDR distribution for RNA-seq sample with edgeR
edgeR RNA-seq FDR
updated 10.0 years ago by 52k • written 10.0 years ago by ▴ 10
14
votes
9
replies
16k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
9.9 years ago gavrielmatt ▴ 30
2
votes
3
replies
3.3k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 15 months ago by 52k • written 15 months ago by • 0
3
votes
3
replies
2.0k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 7.8 years ago by 16k • written 7.8 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 6.4 years ago by 43k • written 6.4 years ago by ▴ 60
0
votes
3
replies
2.1k
views
Redundant meta-features (genes) using FeatureCounts
rna-seq featurecounts
9.9 years ago ccheung • 0
0
votes
3
replies
1.2k
views
Analyzing a subgroups of samples, which result should I trust
deseq2 rna-seq
written 6.6 years ago by ▴ 20
9
votes
12
replies
8.6k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 7 months ago by • 0 • written 9.4 years ago by ▴ 30
3
votes
12
replies
5.6k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 6.2 years ago by ★ 3.0k • written 6.2 years ago by ▴ 10
0
votes
3
replies
3.8k
views
Handling pseudogenes in RNA-seq
rna-seq pseudogenes STAR counts
updated 6.5 years ago by ★ 1.1k • written 6.5 years ago by • 0
5
votes
2
replies
25k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
3
votes
6
replies
2.3k
views
DESeq2 with contaminating cell types
deseq2 rna-seq
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 100
2
votes
5
replies
1.8k
views
Differential Gene Expression
deseq2 bioinformatics rna-seq Tutorial
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
0
votes
3
replies
2.3k
views
How to set the contrast in case of a design of 2 level factor and interaction term.
deseq2 deseq rna-seq
10.0 years ago solgakar@bi.technion.ac.il ▴ 90
4
votes
4
replies
1.6k
views
Correlation analysis taking into account multiple correlations
edger rna-seq correlation
updated 8.2 years ago by ▴ 270 • written 8.2 years ago by ▴ 10
24
votes
11
replies
19k
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 8.9 years ago by 52k • written 8.9 years ago by ▴ 50
3
votes
3
replies
4.9k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 7.3 years ago by 21k • written 7.3 years ago by ▴ 20
3
votes
4
replies
5.5k
views
About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
7.2 years ago David Requena ▴ 20
2
votes
2
replies
2.2k
views
Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
tximport limma rna-seq
updated 7.1 years ago by 43k • written 7.1 years ago by ▴ 50
18
votes
12
replies
4.1k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 9.5 years ago by 43k • written 9.5 years ago by ★ 7.9k
3
votes
6
replies
4.1k
views
edgeR: Error in taglist[[i]] : subscript out of bounds
edger rna-seq
updated 9.4 years ago by 52k • written 9.5 years ago by ▴ 60
12
votes
2
replies
3.8k
views
How does edgeR compare to lme4?
rna-seq edger mixed model random effects lme4
updated 8.5 years ago by 52k • written 8.5 years ago by ▴ 80
1
vote
8
replies
3.4k
views
RNA-seq bacterial transcriptome analysis in EdgeR with unusual dispersion trend
RNA-seq edgeR estimatedispersions bacteria
9.9 years ago • updated 9.8 years ago Mauve • 0
5
votes
3
replies
3.5k
views
Understanding edgeR coefficients and design
edger r edger de rna-seq
updated 9.4 years ago by 52k • written 9.4 years ago by ▴ 30
6
votes
5
replies
2.5k
views
Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
limma rna-seq mixed model repeated measures
updated 6.2 years ago by 52k • written 6.2 years ago by ▴ 280
1
vote
3
replies
2.7k
views
DESeq normalization seems to reverse the directionality of log2FoldChange - is this normal?
deseq2 rnaseq rna-seq normalization cpm
updated 8.6 years ago by ★ 13k • written 8.6 years ago by • 0
10
votes
14
replies
9.2k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
8.4 years ago • updated 8.3 years ago anand_mt ▴ 90
1
vote
13
replies
6.7k
views
"Over-correction" in the size-factors of the DESeq2 package
deseq2 rna-seq normalization
8.7 years ago gil.hornung • 0
3
votes
3
replies
1.3k
views
RNA-seq genes differentially expressed in combined treatment
DESeq2 deseq2 RNA-seq
8.7 years ago david.ashbrook • 0
0
votes
2
replies
3.0k
views
DESeq2 different results from similar datasets
deseq2 differential gene expression rna-seq
9.0 years ago erin.gill81 ▴ 60
4
votes
5
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6.5k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 8.6 years ago by ★ 3.6k • written 8.6 years ago by ▴ 180
4
votes
2
replies
2.7k
views
Quality control on RNA-Seq (level 3) data from TCGA
rna-seq GC-Content qualitycontrol
updated 9.1 years ago by ▴ 180 • written 9.1 years ago by ▴ 60
0
votes
3
replies
1.7k
views
Trouble with Custom PC Plot
deseq2 plotPCA PCA rna-seq
8.6 years ago newsomew13 • 0
9
votes
11
replies
5.9k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 7.8 years ago by ▴ 20 • written 8.7 years ago by ▴ 10
5
votes
7
replies
1.7k
views
Co-expression between host and pathogen genes
edger rna-seq
updated 8.7 years ago by ★ 28k • written 8.7 years ago by ▴ 10
0
votes
2
replies
3.0k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
8.9 years ago hywel.williams • 0
11
votes
8
replies
9.8k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 8.2 years ago by ★ 3.0k • written 8.2 years ago by ▴ 70
3
votes
4
replies
2.9k
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
9.2 years ago moldach ▴ 20
0
votes
4
replies
2.3k
views
Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
7.9 years ago bioinf ▴ 10
0
votes
2
replies
5.0k
views
PlotMA Filters for DeSEQ2 ; adjusting script
deseq2 rnaseq plotMA deseq rna-seq
updated 8.7 years ago by 43k • written 8.7 years ago by • 0
14
votes
9
replies
4.2k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 6.9 years ago by ▴ 130 • written 8.6 years ago by ▴ 80
10
votes
4
replies
4.9k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 8.4 years ago by 52k • written 8.4 years ago by ▴ 110
0
votes
2
replies
4.9k
views
WGCNA - problems picking a suitable power
WGCNA pickSoftThreshold power RNA-Seq
updated 8.8 years ago by ★ 3.0k • written 8.8 years ago by ▴ 10
2
votes
10
replies
2.3k
views
Design matrix for unbalanced data
edgeR RNA-Seq design matrix multifactorial design
8.8 years ago Yogender Gowtham ▴ 20
3
votes
2
replies
1.5k
views
Bayesian Network analysis of gene regulatory relationship
Bayesian network RNA-seq Gene regulatory network
7.3 years ago nancydong20 ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi Gordon, Thank you for pointing out that FeatureCounts detects junction reads de novo. It is not in the manual, and maybe could be. Give…
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2 by Michael Love 43k
I've seen in some papers ~1 TPM for saying something in mouse/human etc. was "minimally expressed". For an average length gene, 10 count…
Answer: Feature Counts - potential bug with outfile.jcounts by Gordon Smyth 52k
The behavior that you have documented is expected and is explained in the featureCounts documentation. The first thing to understand is th…
Answer: Feature Counts -R XS Read Assignment Tag by Gordon Smyth 52k
No, featureCounts cannot change the XS tag to a different tag, because that would change the information in the output. featureCounts needs…
Comment: Margins for gene_set_enrichment_plot by Leonardo Collado Torres ★ 1.1k
Thanks! This one might be worth remaking with `ComplexHeatmap`. Similar to https://github.com/LieberInstitute/spatialLIBD/pull/91 that was …
Votes
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
A: Relations used in GO.db GOBPANCESTOR
Relations used in GO.db GOBPANCESTOR
Answer: RSubread output significantly different from bash Subread output
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