Showing : RNASeq • reset
2
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9
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3.0k
views
Limma: Defining the design matrix of a linear mixed model
rnaseq limma differential expression
9.1 years ago j.baldauf • 0
5
votes
4
replies
10k
views
Choosing a threshold for minimum counts in RNAseq
rnaseq deseq2
updated 8.3 years ago by 43k • written 9.7 years ago by ▴ 20
5
votes
8
replies
6.2k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 9.0 years ago by ▴ 40
25
votes
37
replies
18k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq RSEM TCGA edgeR normalization
updated 9.1 years ago by 53k • written 9.1 years ago by ▴ 840
3
votes
3
replies
2.4k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 9.0 years ago by 16k • written 9.0 years ago by ▴ 10
10
votes
6
replies
12k
views
Estimating and removing batch effects from rna-seq dataset
sva batch effect rnaseq removebatcheffect() limma
updated 10.4 years ago by ▴ 650 • written 10.4 years ago by ▴ 110
4
votes
4
replies
5.9k
views
Rsubread installation issues
rnaseq
11.0 years ago lshepard ▴ 40
22
votes
13
replies
31k
views
gene dispersion, what does it mean?
gener rnaseq
updated 2.9 years ago by 53k • written 10.3 years ago by ▴ 80
0
votes
3
replies
1.8k
views
RNASeq, differential expression between group, and large variance within groups
RNASeq qPCR edgeR DESeq RNASeq qPCR edgeR DESeq
updated 15.0 years ago by ★ 6.0k • written 15.0 years ago by 53k
0
votes
2
replies
1.9k
views
Considering both : batch effect and patient to patient variation in EdgeR analysis
EdgeR batch effect patient rnaseq
10.5 years ago n.deshpande • 0
0
votes
5
replies
5.7k
views
Statistical power of limma vs mixed model approach to analyze microarray and differentialproteomics/peptidomics experiments and Poisson/binomial mixe…
limma maanova rnaseq
12.7 years ago • updated 4.2 years ago Gordon Smyth 53k
0
votes
5
replies
2.1k
views
Mapping short reads to gene IDs in GPL9115
rnaseq EST gene Id
updated 10.3 years ago by 25k • written 10.3 years ago by ▴ 60
1
vote
2
replies
1.2k
views
plotMDS: metric or non-metric method?
edger rnaseq
10.6 years ago martha.nigg.1 • 0
3
votes
5
replies
13k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq normalization tpm tmm
10.4 years ago nickbern92 • 0
2
votes
4
replies
5.1k
views
Number of co-variables k in RUVSeq (RUVr)
rnaseq ruvseq RUVr edgeR
10.2 years ago David R ▴ 90
1
vote
2
replies
3.0k
views
Interaction term logFC
RNASeq GO DESeq2 RNASeq GO DESeq2
updated 11.6 years ago by 68k • written 11.6 years ago by ★ 13k
0
votes
8
replies
4.0k
views
views on Rle using GRanges object
RNASeq Coverage GO rtracklayer RNASeq Coverage GO rtracklayer
updated 14.6 years ago by 16k • written 14.6 years ago by ▴ 740
2
votes
4
replies
4.3k
views
report genes in intersection of Venn diagram with topTable?
rnaseq venn diagram limma toptable edgeR
updated 10.7 years ago by 53k • written 10.7 years ago by • 0
2
votes
6
replies
2.9k
views
derfinder gets stuck in calculatePvalues
derfinder software error rnaseq
10.7 years ago drramki.chop • 0
4
votes
14
replies
10k
views
Extracting custom post-normalization counts from DESeq2
deseq2 r ruvseq normalization rnaseq
10.6 years ago nickp60 • 0
0
votes
4
replies
1.9k
views
Array data vs. Next Gen with log 2 Fold Change
RNASeq Microarray limma RNASeq Microarray limma
updated 14.6 years ago by 53k • written 14.6 years ago by ▴ 560
6
votes
3
replies
4.2k
views
Normalization of RNA-seq data, called remove unwanted variation (RUV), in DESeq2
normalization deseq2 rnaseq
10.8 years ago Silva • 0
2
votes
2
replies
2.2k
views
Help with cummeRbund
cummeRbund Script analysis RNAseq cuffdiff
updated 10.8 years ago by ▴ 370 • written 10.8 years ago by • 0
0
votes
2
replies
4.0k
views
Going crazy with normalizing TCGA raw rsem gene count
cancer tcga normalization rnaseq differential gene expression
updated 7.9 years ago by • 0 • written 10.9 years ago by • 0
6
votes
11
replies
5.1k
views
edgeR on extremely large dataset
edgeR rnaseq
10.2 years ago martiningi ▴ 40
2
votes
2
replies
4.1k
views
Down/Up-regulated genes asymmetry in edgeR differential expression analysis
edgeR rnaseq
10.9 years ago Pauly Lin ▴ 160
9
votes
8
replies
24k
views
Integrating DESeq2 and TopGO for Enrichment
go deseq2 rnaseq r
updated 11.1 years ago by ▴ 610 • written 11.1 years ago by ▴ 20
4
votes
8
replies
3.5k
views
Can't find any differentially expressed genes
rnaseq differential gene expression design matrix edgeR
updated 10.9 years ago by 53k • written 10.9 years ago by ▴ 10
2
votes
2
replies
6.4k
views
DESeq2 factor design vs pair-wise comparison
deseq2 rnaseq
11.1 years ago shin.jx • 0
0
votes
2
replies
2.4k
views
quasR - how are exon identifiers for exon counts determined
rnaseq exon quasr
updated 11.2 years ago by ★ 13k • written 11.2 years ago by • 0
1
vote
3
replies
2.8k
views
summarizeOverlaps bplapply error
genomicalignments genomicranges bioconductor rnaseq
updated 10.6 years ago by • 0 • written 11.1 years ago by • 0
0
votes
3
replies
2.8k
views
How to analyze a known fusion gene expression in RNAseq
fusion genes rnaseq
10.9 years ago stephen66 ▴ 50
21
votes
13
replies
18k
views
Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
edger rnaseq
updated 11.4 years ago by 68k • written 11.4 years ago by ▴ 50
4
votes
5
replies
11k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 11.3 years ago by ★ 13k • written 11.3 years ago by ▴ 10
0
votes
9
replies
3.3k
views
Multifactor analysis in EdgeR and DESeq2 - help setting up similar contrasts in the two packages
edger deseq2 rnaseq
11.4 years ago CT • 0
6
votes
2
replies
3.6k
views
DESeq2: Excluding results of specific contrasts from another set of results
deseq2 rnaseq
11.3 years ago bmansfeld ▴ 10
0
votes
10
replies
3.2k
views
DESeq /edgeR design problem for a small RNASeq
RNASeq edgeR DESeq RNASeq edgeR DESeq
updated 12.7 years ago by 53k • written 12.8 years ago by ▴ 90
0
votes
7
replies
2.1k
views
edgeR: calcNormFactors question
RNASeq RNASeq
13.7 years ago gowtham ▴ 210
1
vote
2
replies
1.9k
views
edgeR design matrix question
edgeR limma rnaseq design and contrast matrix
updated 11.2 years ago by 53k • written 11.2 years ago by • 0
5
votes
6
replies
8.0k
views
proper transformation for differential expression in normalized log expression data
tcga rnaseq deseq2 vsn edger
updated 11.1 years ago by 53k • written 11.2 years ago by • 0
2
votes
3
replies
2.8k
views
SystemPipeR: alignments with ambiguous pairing were dumped.
R rnaseq tophat summarizeoverlaps systempiper
updated 9.3 years ago by ★ 1.7k • written 9.3 years ago by • 0
0
votes
17
replies
4.0k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq Microarray qPCR Coverage edgeR DESeq Sequencing RNASeq Microarray qPCR
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ▴ 330
3
votes
5
replies
2.7k
views
PCA of voom weight values
limma voom rnaseq
updated 11.0 years ago by 53k • written 11.0 years ago by ▴ 140
0
votes
2
replies
2.3k
views
RNAseq expression threshold using DESeq2 normalised counts
RNASeq RNASeq
updated 11.6 years ago by 43k • written 11.6 years ago by ★ 13k
0
votes
6
replies
2.4k
views
design matrix edge R pairwise comparison at different time points after infection with replicates
RNASeq edgeR RNASeq edgeR
updated 13.7 years ago by 53k • written 13.7 years ago by ▴ 70
0
votes
2
replies
1.5k
views
EdgeR - problems running estimateCRDisp
RNASeq edgeR RNASeq edgeR
updated 15.4 years ago by 53k • written 15.4 years ago by ▴ 60
0
votes
2
replies
2.0k
views
Assessing RNA-Seq sample replicates
RNASeq
updated 10.9 years ago by ▴ 80 • written 12.9 years ago by ▴ 100
3
votes
6
replies
3.6k
views
RNAseq multifactor experiment limma design with patient and batch effects
limma rnaseq batcheffect
updated 10.7 years ago by • 0 • written 11.3 years ago by ▴ 10
3
votes
7
replies
2.7k
views
Add up RLEs that are in lists?
RLE GenomicFeatures rnaseq
updated 10.9 years ago by 16k • written 10.9 years ago by ▴ 30
3
votes
4
replies
5.2k
views
What is the easiest way to make the GC content and length matrix for package cqn?
RNASeq edgeR cqn RNASeq edgeR cqn
updated 11.9 years ago by 25k • written 11.9 years ago by ▴ 390
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Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
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SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
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Votes
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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