Showing : RNA-SEQ • reset
1
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14
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9.7k
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DESeq Error in round(assay(se)) : non-numeric argument to mathematical function
deseq rna-seq
8.5 years ago rodriguez.varenka • 0
0
votes
6
replies
1.2k
views
Which sequencing parameters are required for SGSeq analysis of splice events?
rna-seq alternative splicing SGSeq
4.9 years ago andrea.bast • 0
40
votes
44
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9.2k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR p-value DESeq RNA-Seq
updated 5.8 years ago by ▴ 60 • written 6.4 years ago by ▴ 10
3
votes
7
replies
5.1k
views
What does this error mean? - issue implementing SVA
sva rna-seq
updated 5.5 years ago by ▴ 30 • written 7.6 years ago by ▴ 40
1
vote
3
replies
1.8k
views
Gene Ontology and Gene Set Enrichment
rna-seq bioinformatics gene ontology gene set enrichment go
updated 7.0 years ago by ★ 1.2k • written 7.0 years ago by ▴ 10
1
vote
4
replies
2.2k
views
strange FDR distribution for RNA-seq sample with edgeR
edgeR RNA-seq FDR
updated 8.8 years ago by 48k • written 8.8 years ago by ▴ 10
14
votes
9
replies
13k
views
How does DESeq2 handle zero counts in one condition?
deseq2 deseq rna-seq
8.7 years ago gavrielmatt ▴ 30
2
votes
3
replies
191
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 3 days ago by 48k • written 7 days ago by • 0
3
votes
3
replies
1.6k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 6.6 years ago by 16k • written 6.6 years ago by ▴ 10
0
votes
3
replies
738
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3x2 comparisons in DEseq - time (3 time points) and two treatments
deseq2 deseq rna-seq multiple comparisons
updated 5.2 years ago by 40k • written 5.2 years ago by ▴ 60
0
votes
3
replies
1.8k
views
Redundant meta-features (genes) using FeatureCounts
rna-seq featurecounts
8.7 years ago ccheung • 0
0
votes
3
replies
862
views
Analyzing a subgroups of samples, which result should I trust
deseq2 rna-seq
written 5.4 years ago by ▴ 20
9
votes
11
replies
7.0k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 8.2 years ago by 48k • written 8.2 years ago by ▴ 30
3
votes
12
replies
3.7k
views
Batch correction when only some subjects have replicates across batches
limma batch effect rna-seq
updated 5.0 years ago by ★ 2.8k • written 5.0 years ago by ▴ 10
0
votes
3
replies
2.8k
views
Handling pseudogenes in RNA-seq
rna-seq pseudogenes STAR counts
updated 5.3 years ago by 1.1k • written 5.3 years ago by • 0
3
votes
3
replies
1.2k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 4.6 years ago by ★ 2.8k • written 4.6 years ago by ▴ 50
3
votes
6
replies
1.7k
views
DESeq2 with contaminating cell types
deseq2 rna-seq
updated 6.7 years ago by 40k • written 6.7 years ago by ▴ 100
2
votes
5
replies
1.4k
views
Differential Gene Expression
deseq2 bioinformatics rna-seq Tutorial
updated 7.0 years ago by 40k • written 7.0 years ago by ▴ 10
0
votes
3
replies
1.8k
views
How to set the contrast in case of a design of 2 level factor and interaction term.
deseq2 deseq rna-seq
8.8 years ago solgakar@bi.technion.ac.il ▴ 90
4
votes
4
replies
1.2k
views
Correlation analysis taking into account multiple correlations
edger rna-seq correlation
updated 7.0 years ago by ▴ 270 • written 7.0 years ago by ▴ 10
19
votes
11
replies
16k
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 7.6 years ago by 48k • written 7.6 years ago by ▴ 50
3
votes
3
replies
3.5k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 6.1 years ago by 21k • written 6.1 years ago by ▴ 20
3
votes
4
replies
4.4k
views
About the results and contrast (DESeq2)
deseq2 differential expression rna-seq
6.0 years ago David Requena ▴ 20
2
votes
2
replies
1.7k
views
Using tximport to convert a dataframe consisting of tpm to counts for use with limma-voom or edgeR?
tximport limma rna-seq
updated 5.8 years ago by 40k • written 5.8 years ago by ▴ 50
18
votes
12
replies
3.3k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR deseq2 rna-seq independent filtering
updated 8.3 years ago by 40k • written 8.3 years ago by 7.8k
3
votes
6
replies
3.5k
views
edgeR: Error in taglist[[i]] : subscript out of bounds
edger rna-seq
updated 8.2 years ago by 48k • written 8.2 years ago by ▴ 60
12
votes
2
replies
3.1k
views
How does edgeR compare to lme4?
rna-seq edger mixed model random effects lme4
updated 7.2 years ago by 48k • written 7.3 years ago by ▴ 80
1
vote
8
replies
2.9k
views
RNA-seq bacterial transcriptome analysis in EdgeR with unusual dispersion trend
RNA-seq edgeR estimatedispersions bacteria
8.6 years ago Mauve • 0
5
votes
3
replies
2.7k
views
Understanding edgeR coefficients and design
edger r edger de rna-seq
updated 8.2 years ago by 48k • written 8.2 years ago by ▴ 30
6
votes
5
replies
1.7k
views
Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
limma rna-seq mixed model repeated measures
updated 5.0 years ago by 48k • written 5.0 years ago by ▴ 270
1
vote
3
replies
2.0k
views
DESeq normalization seems to reverse the directionality of log2FoldChange - is this normal?
deseq2 rnaseq rna-seq normalization cpm
updated 7.4 years ago by 13k • written 7.4 years ago by • 0
9
votes
14
replies
7.7k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
7.2 years ago • updated 7.1 years ago anand_mt ▴ 80
1
vote
13
replies
5.6k
views
"Over-correction" in the size-factors of the DESeq2 package
deseq2 rna-seq normalization
7.4 years ago gil.hornung • 0
3
votes
3
replies
931
views
RNA-seq genes differentially expressed in combined treatment
DESeq2 deseq2 RNA-seq
7.5 years ago david.ashbrook • 0
0
votes
2
replies
2.4k
views
DESeq2 different results from similar datasets
deseq2 differential gene expression rna-seq
7.8 years ago erin.gill81 ▴ 60
4
votes
5
replies
5.5k
views
Hisat2 vs featureCounts summary statistics
featurecounts hisat2 rna-seq mapping
updated 7.3 years ago by ★ 3.5k • written 7.4 years ago by ▴ 180
4
votes
2
replies
2.1k
views
Quality control on RNA-Seq (level 3) data from TCGA
rna-seq GC-Content qualitycontrol
updated 7.9 years ago by ▴ 180 • written 7.9 years ago by ▴ 60
0
votes
3
replies
1.3k
views
Trouble with Custom PC Plot
deseq2 plotPCA PCA rna-seq
7.3 years ago newsomew13 • 0
9
votes
11
replies
5.2k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 6.6 years ago by ▴ 20 • written 7.4 years ago by ▴ 10
5
votes
7
replies
1.3k
views
Co-expression between host and pathogen genes
edger rna-seq
updated 7.5 years ago by ★ 28k • written 7.5 years ago by ▴ 10
0
votes
2
replies
2.4k
views
WGCNA - Using real data for tutorial III
pathways wgcna network rna-seq
7.7 years ago hywel.williams • 0
11
votes
8
replies
7.7k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 7.0 years ago by ★ 2.8k • written 7.0 years ago by ▴ 70
3
votes
4
replies
2.5k
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
8.0 years ago moldach ▴ 20
0
votes
4
replies
1.7k
views
Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
6.7 years ago bioinf ▴ 10
0
votes
2
replies
4.6k
views
PlotMA Filters for DeSEQ2 ; adjusting script
deseq2 rnaseq plotMA deseq rna-seq
updated 7.5 years ago by 40k • written 7.5 years ago by • 0
14
votes
9
replies
3.3k
views
Is Limma's removeBatchEffect() and log2() commutative?
limma rna-seq removebatcheffect()
updated 5.7 years ago by ▴ 130 • written 7.4 years ago by ▴ 80
10
votes
4
replies
3.8k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 7.2 years ago by 48k • written 7.2 years ago by ▴ 110
0
votes
2
replies
3.4k
views
WGCNA - problems picking a suitable power
WGCNA pickSoftThreshold power RNA-Seq
updated 7.6 years ago by ★ 2.8k • written 7.6 years ago by ▴ 10
2
votes
10
replies
1.7k
views
Design matrix for unbalanced data
edgeR RNA-Seq design matrix multifactorial design
7.6 years ago Yogender Gowtham ▴ 20
3
votes
2
replies
1.1k
views
Bayesian Network analysis of gene regulatory relationship
Bayesian network RNA-seq Gene regulatory network
6.0 years ago nancydong20 ▴ 10
50 results • Page 1 of 1
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Comment: Manual creation of qPCRset does not work by Ed Siefker ▴ 230
Thanks! This works for me.
Answer: Manual creation of qPCRset does not work by James W. MacDonald 63k
``` > mat <- matrix(rnorm(6*96), ncol = 6, nrow = 96, byrow = FALSE) > pd <- new("AnnotatedDataFrame", data = data.frame(1:6, row.names …
Answer: ukb Chromosomal position information was converted into SNPS by James W. MacDonald 63k
In my work, we almost always convert RSIDs to chr:pos because the former is ambiguous and changing whereas the latter is not. Which is like…
Comment: T.fit function of maSigPro returns error message by hanna.g • 0
Addition to the issue above: the T.fit function works only when choosing the step.method = "forward", for whatever reason. Maybe this clue …
Answer: Deseq2, enrichGO and ensembl ID by James W. MacDonald 63k
1. There isn't a keytype alternative. You need the gene IDs. 2. Convert the `rownames` of your 'se' object, or the `rownames` of your `D…
Votes
Answer: Manual creation of qPCRset does not work
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
Answer: comparing contrasts in edger/lima using makeContrasts function
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Popular Question to James W. MacDonald 63k
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