Showing : RnaSeq • reset
17
votes
14
replies
54k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 3.6 years ago by • 0 • written 8.5 years ago by ▴ 20
52
votes
20
replies
52k
views
Batch correction in DESeq2
rnaseq batch effect deseq2 combat removebatcheffect()
updated 9.6 years ago by • 0 • written 10.1 years ago by ▴ 110
19
votes
6
replies
50k
views
How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
rnaseq annotationdbi
updated 9.3 years ago by ★ 6.8k • written 9.3 years ago by ▴ 70
17
votes
4
replies
33k
views
RPKM, CPM and TMM
edger rnaseq differential expression
updated 10.6 years ago by ★ 29k • written 10.6 years ago by ▴ 160
22
votes
13
replies
31k
views
gene dispersion, what does it mean?
gener rnaseq
updated 2.8 years ago by 53k • written 10.2 years ago by ▴ 80
3
votes
7
replies
30k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 6.9 years ago by 43k • written 6.9 years ago by • 0
1
vote
19
replies
30k
views
Import bamfiles for RNAsequencing analysis
R rnaseq bam file
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 10
5
votes
8
replies
29k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 17 months ago by ▴ 60 • written 3.6 years ago by ▴ 30
8
votes
10
replies
27k
views
Design formula and Design matrix in DESeq
rnaseq deseq2 formula Limma
10.7 years ago AurelieMLB ▴ 50
4
votes
3
replies
25k
views
Fisher test in Rna seq
rna-seq rnaseq r
updated 6.5 years ago by 53k • written 7.1 years ago by • 0
0
votes
4
replies
24k
views
DESeq2: How do I compare certain samples that are in two groups and two treatments
deseq2 rnaseq R
8.7 years ago zeynep.nenseth • 0
9
votes
8
replies
23k
views
Integrating DESeq2 and TopGO for Enrichment
go deseq2 rnaseq r
updated 11.0 years ago by ▴ 610 • written 11.0 years ago by ▴ 20
3
votes
6
replies
23k
views
DESeq2: QQ plot of P-values
deseq2 rnaseq rna-seq
8.5 years ago nikmehr22 • 0
32
votes
16
replies
22k
views
difference among tximport scaledTPM, lengthScaledTPM and the original TPM output by salmon/kallisto
tximport deseq2 TPM RPKM rnaseq
updated 7.7 years ago by ▴ 20 • written 9.5 years ago by ▴ 200
6
votes
12
replies
20k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 10
11
votes
1
reply
19k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq deseq2
updated 10.2 years ago by 43k • written 10.2 years ago by ▴ 20
8
votes
10
replies
18k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 9 months ago by ★ 5.0k • written 9.5 years ago by ▴ 20
0
votes
4
replies
18k
views
3D PCA Plot of RNA-seq Data using plotPCA from within DESeq2
deseq2 rnaseq PCA
updated 10.8 years ago by 43k • written 10.8 years ago by ▴ 60
21
votes
13
replies
18k
views
Obtaining Differentially expressed gene lists at a Fold change and FDR cut-off
edger rnaseq
updated 11.2 years ago by 68k • written 11.2 years ago by ▴ 50
27
votes
7
replies
17k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq deseq2 ercc
updated 9.3 years ago by ★ 3.8k • written 9.3 years ago by ▴ 30
25
votes
37
replies
17k
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 9.0 years ago by 53k • written 9.0 years ago by ▴ 840
3
votes
2
replies
17k
views
how to calculate gene length to be used in rpkm() in edgeR
RNASeq edgeR rpkm
updated 2.8 years ago by 53k • written 11.7 years ago by ★ 1.0k
0
votes
9
replies
17k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2 pvalue visualization enhancedvolcano rnaseq
written 7.0 years ago by • 0
1
vote
13
replies
16k
views
Count matrix from Kallisto as input for DESeq2
rnaseq deseq2 kallisto
9.4 years ago yjliu1127 • 0
7
votes
8
replies
16k
views
DESeq2: one condition vs multiple combined
rnaseq deseq2
updated 7.8 years ago by ▴ 10 • written 9.4 years ago by ▴ 40
28
votes
7
replies
14k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 2.3 years ago by ▴ 10 • written 8.3 years ago by ▴ 40
1
vote
6
replies
14k
views
Change fontsize/remove name of annotation ComplexHeatmap package
r rnaseq complexHeatmap annotation
updated 5.6 years ago by ▴ 290 • written 5.6 years ago by ▴ 10
9
votes
7
replies
14k
views
What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
deseq2 rnaseq pca tsne
updated 8.6 years ago by ▴ 10 • written 8.6 years ago by ▴ 30
6
votes
6
replies
14k
views
Why different filtering criteria using CPM to filter the RNA-seq count data in edgeR have so much influence on the number of DE genes?
rnaseq edger
8.3 years ago Jack ▴ 20
26
votes
7
replies
13k
views
Different logFC (log2foldchange) values for genes from limma-voom and other tools (edgeR and DESeq2)
limma deseq2 edger rnaseq
updated 8.3 years ago by 53k • written 8.3 years ago by ▴ 20
9
votes
6
replies
13k
views
Error bars DESeq or DESeq2 fold change
rnaseq deseq2 deseq standard error confidence interval
updated 4.2 years ago by 43k • written 9.8 years ago by ▴ 10
1
vote
1
reply
13k
views
Deseq2 for RNAseq experiments without replicates
rnaseq deseq2
updated 10.0 years ago by 43k • written 10.0 years ago by • 0
4
votes
6
replies
13k
views
How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
DESeq2 RNASeq RNASeqData
3.9 years ago treebig44 ▴ 40
6
votes
2
replies
13k
views
DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
deseq2 R rnaseq
updated 10.0 years ago by 43k • written 10.0 years ago by • 0
3
votes
5
replies
13k
views
Normalization of RNA-seq data: between samples and within samples
rnaseq normalization tpm tmm
10.3 years ago nickbern92 • 0
3
votes
11
replies
13k
views
How to interpret plotBCV plots in edgeR
rnaseq edger
8.9 years ago davide.bau • 0
5
votes
7
replies
13k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 2.0 years ago by • 0 • written 8.8 years ago by • 0
4
votes
5
replies
12k
views
DESeq2 Following RSEM
deseq2 rnaseq
updated 8.8 years ago by 43k • written 8.9 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 10.3 years ago by ▴ 650 • written 10.3 years ago by ▴ 110
5
votes
4
replies
12k
views
DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 3.8 years ago by • 0 • written 4.4 years ago by ▴ 10
9
votes
12
replies
11k
views
Filtering of RNA-seq data in EdgeR
rnaseq edger filtering
written 9.7 years ago by ▴ 20
0
votes
5
replies
11k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 22 months ago by • 0 • written 9.3 years ago by • 0
3
votes
9
replies
11k
views
merge fastq.gz in R? (or in Windows?)
rnaseq bioconductor fastq
updated 5.1 years ago by • 0 • written 10.5 years ago by • 0
4
votes
5
replies
11k
views
limma voom accessing normalised counts tables
limma rnaseq geneexpression voom counts
updated 11.2 years ago by ★ 13k • written 11.2 years ago by ▴ 10
2
votes
6
replies
11k
views
Estimation of dispersion in DeSeq and DeSeq2
deseq deseq2 rnaseq
updated 11.2 years ago by 43k • written 11.2 years ago by ▴ 10
1
vote
6
replies
11k
views
Getting HGNC gene names from Ensembl transcript IDs (e.g., ENST0000...)
rnaseq r biomart
updated 10.2 years ago by ★ 2.1k • written 10.2 years ago by ▴ 40
1
vote
1
reply
11k
views
Undertanding how DESeq2 handles multiple test conditions
rnaseq deseq2 r
updated 11.0 years ago by ★ 7.9k • written 11.0 years ago by ▴ 20
3
votes
3
replies
11k
views
Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
rnaseq rna-seq limma geoquery edger
updated 8.4 years ago by 21k • written 8.4 years ago by ▴ 20
4
votes
14
replies
10k
views
Extracting custom post-normalization counts from DESeq2
deseq2 r ruvseq normalization rnaseq
10.5 years ago nickp60 • 0
3
votes
4
replies
10k
views
DESeqDataSetFromMatrix giving error: "argument must be coercible to non-negative integer"
DESeqDataSet DESeqDataSetFromMatrix rnaseq deseq2
9.6 years ago ErickF ▴ 40
1,412 results • Page 1 of 29
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
My apologies, I forgot that `design.group` is not included in the final matrix, because the baseline group effects are already captured by …
Answer: Bile acid analysis with limpa by Gordon Smyth 53k
I am not familiar with targeted HPLC-MS and I don't know what you mean by "peak areas". If it produces standard format mass spec data from …
Comment: How to convert .raw data for use in xcms by TikTsossa33ssalpc • 0
It sounds like your mzML conversion has a CV term that XCMS doesn t recognize, which often happens with newer vendor formats or outdated ms…
Comment: Boolean Gate Combination for Any 2 Positive Events in flowWorkspace by TikTsossa33ssalpc • 0
To calculate event numbers for boolean combinations in flow cytometry, you should use a logic gating tool or a script that processes popula…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Confirming my understanding after executing the code provided: this is similar to a design formula of `~0+mouse+group+group:allele`, except…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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