Showing : RNA-Seq • reset
2
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2.8k
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Correcting for Batch Effects Prior to Differential Gene Expression Analysis with limma
limma batch effect rna-seq
updated 8.3 years ago by ★ 29k • written 8.3 years ago by • 0
0
votes
7
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3.1k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 3.9 years ago by • 0 • written 8.4 years ago by ▴ 40
1
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4
replies
1.6k
views
DESeq2: Tests of log2 differences
deseq2 rna-seq transcription dgea
8.4 years ago fabian ▴ 40
0
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1
reply
1.3k
views
can I extract data for subset of cancer types from GSE62944
limma rna-seq
updated 8.4 years ago by ▴ 130 • written 8.4 years ago by • 0
1
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5
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3.6k
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RNA-seq analysis on mouse data with human contamination in controls
rna-seq salmon tximport limma
updated 8.4 years ago by ★ 29k • written 8.4 years ago by ▴ 70
3
votes
3
replies
1.6k
views
Subsetting ELists and Applying sva to Iterative Differential Gene Expression Tests
limma edgeR sva RNA-Seq
updated 8.4 years ago by 53k • written 8.5 years ago by • 0
3
votes
6
replies
2.4k
views
Regressing effect of treatment on RNA-seq expected count from rsem.
RNA rna-seq science bioinformatics
updated 8.5 years ago by 68k • written 8.5 years ago by ▴ 20
0
votes
1
reply
1.2k
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Bioconductor RNA-seq bed file read-in/download then wavelet transform
bed files wavelet rna-seq
updated 8.5 years ago by 4.2k • written 8.5 years ago by • 0
2
votes
2
replies
2.8k
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Pairwise differential expression analysis with batch effect using edgeR and SVA
edger rna-seq sva differential expression
updated 8.5 years ago by ★ 29k • written 8.5 years ago by • 0
5
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3
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2.8k
views
Correct contrast for testing multi-level interaction effect in limma using combined factors design matrix
limma contrast matrix limma design matrix limma rna-seq limma voom
updated 8.5 years ago by ★ 29k • written 8.5 years ago by • 0
1
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2
replies
2.4k
views
How to proceed with different degradation levels of RNA-seq samples?
degradation RNA-seq variability differential expression brain
updated 8.5 years ago by ★ 29k • written 8.5 years ago by ▴ 90
0
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1
reply
1.5k
views
makeTxDbFromGFF returns object with wrong seqids (wrong chromosome names)
genomicfeatures txdb canis familiaris rna-seq
updated 8.5 years ago by 68k • written 8.5 years ago by • 0
0
votes
13
replies
2.4k
views
Understanding differences in results with and without setting of pairing factor
DESeq2 deseq2 rna-seq paired samples
updated 8.5 years ago by 43k • written 8.5 years ago by ▴ 90
1
vote
3
replies
1.9k
views
How different ploidy affect differential expression analysis with RNA-seq
ploidy normalization rna-seq differential expression assumption
updated 8.5 years ago by ★ 29k • written 8.5 years ago by ▴ 90
1
vote
5
replies
3.5k
views
Force DESeq2 to use pseudocounts
deseq2 rna-seq
8.5 years ago manuelw • 0
1
vote
1
reply
1.3k
views
RIPseeker peak calling parameters for TruSeq Samll RNA stranded library
RIPseeker RIP rna-seq
8.5 years ago ofonov ▴ 10
6
votes
7
replies
5.5k
views
Dealing with (blood) contamination in RNA-seq data
rnaseq rna-seq linear model limma
updated 8.6 years ago by ★ 29k • written 8.6 years ago by ▴ 90
3
votes
3
replies
1.9k
views
Question regarding best bioconductor package for RNA-seq
rna-seq packages
updated 8.6 years ago by ▴ 370 • written 8.6 years ago by ▴ 10
3
votes
2
replies
4.0k
views
Using the ERCC spike as a normalization factor for a custom algorithm
ERCC rna-seq edgeR tmm normalised values
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
3
votes
3
replies
2.2k
views
Comparing two RNAseq experiments using summarizeOverlaps
summarizeoverlaps R bioconductor rnaseq rna-seq
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 10
9
votes
11
replies
6.2k
views
Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport Kallisto rna-seq
updated 8.6 years ago by ▴ 20 • written 9.5 years ago by ▴ 10
6
votes
4
replies
2.8k
views
RNA-seq Normalisation - normalise all samples in experiment or only the ones used in the comparison?
rna-seq normalization edgeR limma
updated 8.6 years ago by 53k • written 8.6 years ago by • 0
1
vote
1
reply
1.3k
views
RNA-Seq comparisons of various sample
RNA-Seq
updated 8.6 years ago by ★ 29k • written 8.6 years ago by • 0
1
vote
2
replies
3.2k
views
topGO for Gene Ontology and Gene Set enrichment
topgo gene ontology gene set enrichment rna-seq bioinformatics
updated 8.7 years ago by ▴ 760 • written 9.0 years ago by ▴ 10
3
votes
6
replies
2.8k
views
DESeq2 with contaminating cell types
deseq2 rna-seq
updated 8.7 years ago by 43k • written 8.7 years ago by ▴ 100
0
votes
2
replies
2.8k
views
HISAT-StringTie-Ballgown, order of biological replicates in script design
ballgown rna-seq
updated 8.7 years ago by ▴ 210 • written 8.7 years ago by • 0
0
votes
4
replies
2.6k
views
Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
8.8 years ago • updated 8.7 years ago bioinf ▴ 10
0
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0
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1.1k
views
Problem annotating with COHCAP 1.16.0 in MacOsX
illimina 450k methylation RNA-seq COHCAP
8.8 years ago IOM ▴ 20
0
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1
reply
1.7k
views
Drug datasets for RNA-seq
rna-seq data
updated 8.8 years ago by 53k • written 8.8 years ago by ▴ 20
4
votes
9
replies
2.0k
views
RNA-seq analysis edgeR
rna-seq edger
updated 8.9 years ago by ★ 7.9k • written 8.9 years ago by ▴ 20
1
vote
1
reply
825
views
Limma MDS plot donor effect
limma rna-seq
updated 8.9 years ago by ★ 29k • written 8.9 years ago by ▴ 20
2
votes
1
reply
3.7k
views
how to plot PCA for only one of two groups compared or plot three groups at a time
deseq2 bioconductor rna-seq pca
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 20
3
votes
7
replies
1.9k
views
edgeR RNA-seq analysis using glm
edger rna-seq
updated 8.9 years ago by ★ 7.9k • written 8.9 years ago by ▴ 20
2
votes
3
replies
3.6k
views
Analysis of RNA-seq time series with edgeR
edger rna-seq differential expression timecourse time course
updated 8.9 years ago by ★ 29k • written 8.9 years ago by • 0
0
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0
replies
1.5k
views
Job: Seeking computational biologists with expertise in RNA-Seq and/or statistics at Immuneering Corporation, Cambridge MA and New York NY
rna-seq CNS Neurodegeneration statistics computational biology Job
8.9 years ago mmartin ▴ 20
1
vote
3
replies
1.4k
views
the output DEGs of limma analyzing RNA-seq data is just 1/3 of those by Tophat-CuffDiff
differential gene expression voom limma RNA-seq
updated 9.0 years ago by 53k • written 9.0 years ago by • 0
1
vote
5
replies
2.3k
views
How to filter tximport output for edgeR?
tximport edger salmon rna-seq
updated 9.0 years ago by 43k • written 9.0 years ago by • 0
8
votes
1
reply
4.3k
views
Using R package 'limma' on pre-normalized counts and the effect of non-equivalent reads/sample on limma linear model
limma rna-seq multi-mapped reads normalization microbiome
updated 9.0 years ago by ★ 13k • written 9.0 years ago by ▴ 30
1
vote
3
replies
2.9k
views
Gene Ontology and Gene Set Enrichment
rna-seq bioinformatics gene ontology gene set enrichment go
updated 9.0 years ago by ★ 1.2k • written 9.0 years ago by ▴ 10
2
votes
10
replies
13k
views
adjusted p-values and p-values problems!
pvalue adjusted pvalue r bonferroni rna-seq
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 10
1
vote
5
replies
5.3k
views
WGCNA - How to prevent "blockwiseModules" command from dividing genes into multiple blocks?
WGCNA RNA-Seq
updated 9.0 years ago by ★ 3.0k • written 9.0 years ago by ▴ 70
2
votes
5
replies
2.1k
views
Differential Gene Expression
deseq2 bioinformatics rna-seq Tutorial
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 10
5
votes
3
replies
3.5k
views
Analyzing RNA-seq data by WGCNA
wgcna rna-seq
updated 9.0 years ago by ★ 3.0k • written 9.0 years ago by ▴ 20
11
votes
8
replies
11k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA RNA-Seq DESeq2 voom removebatcheffect()
updated 9.0 years ago by ★ 3.0k • written 9.0 years ago by ▴ 70
1
vote
2
replies
1.7k
views
RNA-seq time series data analysis
RNA-seq Log-linear Main effects
updated 9.1 years ago by ★ 29k • written 9.1 years ago by • 0
4
votes
4
replies
1.9k
views
Correlation analysis taking into account multiple correlations
edger rna-seq correlation
updated 9.1 years ago by ▴ 280 • written 9.1 years ago by ▴ 10
0
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3
replies
1.5k
views
Incorporate "batch" information for paired-design ?
RNA-Seq deseq2 batch effect
9.1 years ago g.atla ▴ 10
5
votes
3
replies
3.8k
views
Error when calculating DE using the classical approach in edgeR
edgeR differential expression rna-seq
updated 9.1 years ago by 53k • written 9.1 years ago by • 0
10
votes
14
replies
10k
views
too many genes with low read-counts as differential expressed in DESeq2
deseq2 rna-seq
9.2 years ago • updated 9.1 years ago anand_mt ▴ 90
1
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0
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2.0k
views
Pre-processing of RNA sequencing data for GSVA
rnaseq rna-seq preprocessing gsva
9.1 years ago t.kuilman ▴ 170
418 results • Page 7 of 9
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Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 4.9k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 4.9k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Answer: How to model DE for RNA-seq in concordant monozygotic twins? by Gordon Smyth 53k
Your question is more about science than it is about software syntax, and I can't give advice about how to conduct a scientific analysis, n…
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Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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