Showing : RNAseq • reset
25
votes
7
replies
11k
views
Effect of lfcThreshold on p-value in DESeq2
deseq2 rnaseq statistics
updated 6 months ago by ▴ 10 • written 6.5 years ago by ▴ 30
7
votes
2
replies
776
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
6
votes
7
replies
751
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
5
votes
7
replies
1.0k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 3 months ago by 50k • written 13 months ago by • 0
5
votes
15
replies
5.0k
views
Cross-species RNA-seq with DESeq2
deseq2 rnaseq across species
updated 10 months ago by 65k • written 6.8 years ago by ▴ 10
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.1 years ago by ▴ 40
5
votes
7
replies
10.0k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 3 months ago by • 0 • written 7.1 years ago by • 0
4
votes
2
replies
1.2k
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
4
votes
2
replies
600
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
4
votes
6
replies
565
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
4
votes
4
replies
2.0k
views
Unlog transformed data in DESeq2
RNASeq DESeq2 vst rlog Normalization
updated 4 months ago by 50k • written 2.4 years ago by ▴ 10
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 7 months ago by 50k • written 22 months ago by ▴ 30
4
votes
16
replies
7.3k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 5 weeks ago by • 0 • written 8.9 years ago by ▴ 150
4
votes
12
replies
3.7k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 7 months ago by • 0 • written 3.2 years ago by • 0
3
votes
5
replies
828
views
Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
3
votes
6
replies
512
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
9 weeks ago boczniak767 ▴ 720
3
votes
1
reply
127
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 days ago by 50k • written 9 days ago by • 0
3
votes
5
replies
608
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 7 weeks ago by 41k • written 9 weeks ago by ▴ 10
3
votes
4
replies
704
views
Anova table edgeR limma
limma RNASeq edgeR
11 months ago KATHERINE CHUERE NUNES • 0
3
votes
11
replies
2.4k
views
Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
11 months ago • updated 10 months ago Anna ▴ 20
3
votes
1
reply
274
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 3 months ago by 50k • written 3.0 years ago by ▴ 60
2
votes
4
replies
556
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
2
votes
2
replies
250
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
6 weeks ago Sabiha ▴ 20
2
votes
4
replies
595
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
5 months ago Tyler Sagendorf ▴ 10
2
votes
4
replies
1.2k
views
RNAseq : identical sample-sample distances after using limma::removeBatchEffect
DESeq2 RNASeq BatchEffect limma
updated 8 months ago by 41k • written 2.9 years ago by • 0
2
votes
3
replies
1.1k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 4 months ago by ★ 1.3k • written 4 months ago by • 0
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 months ago mohammedtoufiq91 ▴ 10
2
votes
1
reply
703
views
Grouping DEGs yields varying results
RNASeq limma
updated 9 months ago by 50k • written 9 months ago by ▴ 10
2
votes
2
replies
388
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
11 weeks ago jackafiore • 0
2
votes
2
replies
394
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
5 months ago Manthos • 0
2
votes
1
reply
248
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 8 weeks ago by 41k • written 8 weeks ago by ▴ 10
2
votes
8
replies
1.7k
views
Error in Create switchAnalyzeRlist
AlternativeSplicing RNASeq IsoformSwitchAnalyzeR gtf
written 20 months ago by ▴ 10
2
votes
3
replies
456
views
DESeq2 estimateSizeFactors iterate takes too long
RNASeq DESeq2
5 months ago Karthik • 0
1
vote
2
replies
440
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
1
vote
3
replies
346
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 7 weeks ago by ★ 1.3k • written 8 weeks ago by ▴ 10
1
vote
3
replies
790
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 11 months ago by 50k • written 12 months ago by • 0
1
vote
8
replies
2.5k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 4 months ago by • 0 • written 3.3 years ago by ▴ 10
1
vote
3
replies
821
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 3 days ago by ★ 1.2k • written 14 months ago by ▴ 10
1
vote
1
reply
1.4k
views
News: Bioinformatics Summer School - July 2019 - UCLouvain (Belgium)
RNAseq deseq2 proteomics transcriptomics workshop News
written 5.2 years ago by 1.6k
1
vote
6
replies
894
views
Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
1
vote
1
reply
444
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
1
vote
3
replies
558
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 3 months ago by • 0
1
vote
1
reply
370
views
Using DESeq2 statistical framework with to identify differentially expressed loci instead of genes
rnaseq DESeq2
updated 5 months ago by 41k • written 5 months ago by • 0
1
vote
4
replies
613
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
5 months ago Wending • 0
1
vote
2
replies
424
views
RNASeq time course analysis, missing time points for control
RNASeqData RnaSeqSampleSize RNASeq RNASeqPower
4 months ago drewhaydensteele • 0
1
vote
4
replies
295
views
DESeq2 Replicates
DESeq2 RNASeq
7 weeks ago kcarey • 0
1
vote
4
replies
1.9k
views
ComBat Normalisation - data is integers and some floats, confused?!
combat rnaseq combatnormalisation jeffleek sva
updated 6 months ago by • 0 • written 3.1 years ago by • 0
1
vote
2
replies
1.1k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 11 months ago by • 0
50 results • Page 1 of 1
Recent ...
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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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