Showing : RnaSeq • reset
1
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169
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RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
7 days ago • updated 6 days ago drewhaydensteele • 0
3
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2
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186
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limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 10 days ago by 49k • written 10 days ago by • 0
0
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3
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196
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
18 days ago • updated 10 days ago Karthik • 0
0
votes
1
reply
171
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Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 13 days ago by 41k • written 16 days ago by • 0
2
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3
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168
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DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
17 days ago • updated 12 days ago Karthik • 0
2
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2
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186
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
20 days ago • updated 19 days ago Manthos • 0
2
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4
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315
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limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
25 days ago • updated 24 days ago Tyler Sagendorf ▴ 10
0
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1
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227
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DESeq2 model for two genome system
RNASeq DESeq2
updated 4 weeks ago by 41k • written 7 weeks ago by • 0
0
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2
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242
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TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 4 weeks ago by ★ 1.0k • written 6 weeks ago by ▴ 190
0
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9
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2.2k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 4 weeks ago by • 0 • written 6.1 years ago by ▴ 60
1
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4
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356
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
5 weeks ago Wending • 0
0
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0
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146
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
5 weeks ago mch • 0
4
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2
replies
269
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DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 5 weeks ago by 49k • written 6 weeks ago by ▴ 10
0
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6
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395
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DESeq2 Normalization with 4 Groups
Normalization RNASeq DESeq2
6 weeks ago erika.maldonado-rosado • 0
0
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0
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155
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is Dada2 biased toward a particular sequence ?
virology dada2 amplican Sequencing RNASeq
7 weeks ago Sara • 0
0
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2
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418
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Will DESeq2 be appropriate tool for analysis?
RNASeq DESeq2
7 weeks ago • updated 6 weeks ago Karthik • 0
0
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0
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143
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Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
7 weeks ago Florian • 0
0
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0
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142
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Pysam pileup and Rsamtools pileup output discrepancy
Pysam pileup Rsamtools RNASeq
7 weeks ago Xinqi • 0
0
votes
0
replies
153
views
Using DADA2 for finding viral sequence variants
VariantDetection dada2 RNASeq
7 weeks ago Sara • 0
1
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1
reply
233
views
Multiple comparison using DESeq2
RNASeqData RNASeq DESeq2
updated 7 weeks ago by 64k • written 7 weeks ago by • 0
1
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7
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485
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 6 days ago by 49k • written 8 weeks ago by • 0
0
votes
2
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240
views
Issues with ddseq2 for treatment response factoring in different KO clones
Clonality RNASeq DESeq2
updated 8 weeks ago by ★ 1.3k • written 8 weeks ago by • 0
0
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1
reply
244
views
Comparing RNASeq data from multiple studies
RNASeqData RnaSeqSampleSize RNASeqPower RNASeq
updated 9 weeks ago by ▴ 740 • written 10 weeks ago by • 0
3
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5
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405
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 12 weeks ago by ★ 3.6k • written 12 weeks ago by • 0
1
vote
1
reply
251
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 3 months ago by ★ 3.6k • written 3 months ago by • 0
0
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1
reply
397
views
DESeq design and contrast with multiple factors
RNASeq DESeq2
updated 3 months ago by 41k • written 3 months ago by • 0
1
vote
6
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562
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 3 months ago by ★ 3.6k • written 3 months ago by • 0
5
votes
7
replies
485
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 4 months ago by 49k • written 4 months ago by ▴ 10
0
votes
1
reply
792
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 4 months ago by 64k • written 4 months ago by • 0
2
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1
reply
426
views
Grouping DEGs yields varying results
RNASeq limma
updated 4 months ago by 49k • written 4 months ago by ▴ 10
2
votes
5
replies
764
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
4 months ago mohammedtoufiq91 ▴ 10
0
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2
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450
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Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
4 months ago Matteo • 0
3
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2
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649
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 5 months ago by 49k • written 5 months ago by ▴ 10
0
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3
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421
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Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 5 months ago by 64k • written 5 months ago by • 0
3
votes
11
replies
1.4k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
6 months ago Anna ▴ 20
1
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9
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4.7k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 5.8 years ago by • 0
0
votes
1
reply
406
views
CI for logCPM (fitted values)
RNAseq edgeR
updated 6 months ago by 49k • written 6 months ago by ▴ 10
3
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4
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539
views
Anova table edgeR limma
limma RNASeq edgeR
7 months ago KATHERINE CHUERE NUNES • 0
1
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2
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440
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 7 months ago by 49k • written 7 months ago by • 0
0
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3
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567
views
Account for heteroscedasticity when fitting gene expression data
RNAseq
updated 7 months ago by 41k • written 7 months ago by • 0
0
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2
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606
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 7 months ago by • 0
1
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3
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567
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 7 months ago by 49k • written 7 months ago by • 0
0
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2
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694
views
model matrix not full rank
DESeq2 RNASeq
updated 7 months ago by • 0 • written 7 months ago by • 0
0
votes
1
reply
353
views
What is the correct way to split genex_high and genex_low groups for DE analysis?
DESeq2 RNASeq
updated 7 months ago by 41k • written 8 months ago by • 0
2
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3
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413
views
RNA seq with edgeR with several factors
RNAseq factors
7 months ago Nathalie ▴ 20
0
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3
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600
views
edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 7 months ago by 49k • written 7 months ago by • 0
7
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8
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10.0k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 7 months ago by ★ 3.6k • written 7.4 years ago by ▴ 20
0
votes
4
replies
570
views
Combine RNA-seq
BatchEffect R rnaseq
updated 7 months ago by ★ 1.3k • written 7 months ago by • 0
1
vote
1
reply
401
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 7 months ago by 49k • written 7 months ago by • 0
3
votes
12
replies
1.0k
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 7 months ago by 41k • written 7 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Can the limma package be applied to Log2 RUV-normalized data? by Gordon Smyth 49k
515 samples is certainly large enough.
Comment: Correct the batch effect in methylation analysis in R by kyj2226 • 0
Thank you for your kind response Gordon! :) Have a good time at the end of the year! Best, Yujin Kim
Comment: Agilent Microarray Gene Oncology analysis gone wrong by SamGG ▴ 320
Gordon said to let coef to its default value: topTable(fit, n=20)
Comment: Can the limma package be applied to Log2 RUV-normalized data? by Shaimaa Gamal • 0
Hi Gordon, On what basis we can determine whether the dataset is large or not? I am working on a dataset of 515 samples and 5440 genes. I w…
Comment: Agilent Microarray Gene Oncology analysis gone wrong by samagbeyimodupe • 0
Thank you for the quick response. i ran the codes again and removed all the other arguments for eBayes except for fit. I ran the line of co…
Votes
Answer: Correct the batch effect in methylation analysis in R
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Answer: Correct the batch effect in methylation analysis in R
Answer: enrichGOgradient color change
Answer: Filter genes by expression for voomLmFit
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