Showing : DifferentialExpression • reset
9
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6.5k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 12 weeks ago by ★ 4.1k • written 2.1 years ago by ▴ 30
6
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11
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1.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
14 months ago mohammedtoufiq91 ▴ 10
6
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3
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1.6k
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differential gene expression
limma differentialexpression
updated 9.6 years ago by ▴ 760 • written 9.6 years ago by ▴ 20
5
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3
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702
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 5 weeks ago by 50k • written 5 weeks ago by ▴ 50
5
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6
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412
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 18 days ago by ★ 4.1k • written 22 days ago by ▴ 30
5
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9
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1.6k
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Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 2.8 years ago by 65k • written 2.8 years ago by ▴ 830
5
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2
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2.2k
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Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 20 months ago by 50k • written 2.7 years ago by ▴ 10
5
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6
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541
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
5
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6
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1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
4
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6
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580
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 12 weeks ago by 50k • written 3 months ago by • 0
4
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4
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7.3k
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DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 2.1 years ago by • 0 • written 2.7 years ago by • 0
4
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2
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1.7k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 15 months ago by ★ 4.1k • written 15 months ago by ▴ 10
4
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5
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1.7k
views
What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 2.0 years ago by • 0 • written 2.2 years ago by ▴ 30
4
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3
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348
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
4
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10
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1.3k
views
Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
3.5 years ago Hajar • 0
4
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3
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1.2k
views
Limma/voom analysis of time-series data (with only 1 condition)
limma DifferentialExpression
updated 2.2 years ago by 65k • written 2.2 years ago by • 0
4
votes
2
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6.7k
views
DESeq2: removing levels from a factor or not having them in the analysis at all
deseq2 differentialexpression
updated 9.6 years ago by 41k • written 9.6 years ago by ▴ 90
3
votes
1
reply
288
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
3
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6
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2.2k
views
Repeated measures per individual and unbalanced number of measures per individual: DE between groups still an ordinary two-group comparison?
differentialexpression deseq2 limma edger repeatedmeasures
4.6 years ago • updated 2.3 years ago hermidalc ▴ 20
3
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7
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1.4k
views
Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 3.2 years ago by 50k • written 3.2 years ago by ▴ 30
3
votes
7
replies
1.5k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 18 months ago by 50k • written 18 months ago by • 0
3
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6
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1.3k
views
do I have to do this step in creating DGEList ?
DifferentialExpression
updated 14 months ago by 50k • written 14 months ago by • 0
3
votes
2
replies
288
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
12 weeks ago • updated 11 weeks ago Shaimaa Gamal • 0
3
votes
3
replies
947
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 11 months ago by ★ 1.3k • written 11 months ago by ▴ 20
3
votes
5
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4.7k
views
How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
2.7 years ago • updated 2.6 years ago zhxiaokang ▴ 20
3
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4
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1.3k
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How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
2.1 years ago mohammedtoufiq91 ▴ 10
3
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4
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415
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by ▴ 50
3
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8
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3.4k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.0 years ago by ▴ 10
3
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6
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1.3k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 3.4 years ago by 41k • written 3.4 years ago by ▴ 50
3
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3
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568
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comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
3
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6
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1.4k
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 17 months ago by • 0
2
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6
replies
961
views
How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 10 months ago by 3.8k • written 11 months ago by • 0
2
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3
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363
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
2
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2
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1.0k
views
Complex contrasts in limma
RNASeq limma DifferentialExpression
2.2 years ago tcalvo ▴ 90
2
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3
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1.4k
views
DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
2
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2
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1.6k
views
DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
2.9 years ago SUMIT • 0
2
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4
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815
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 15 months ago by 41k • written 15 months ago by • 0
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
2
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2
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941
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edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData miRNA DifferentialExpression edgeR
24 months ago Sarah • 0
2
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2
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870
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Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 12 months ago by ★ 4.1k • written 12 months ago by ▴ 30
2
votes
1
reply
212
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 12 weeks ago by 41k • written 3 months ago by ▴ 20
2
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4
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506
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
2
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4
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1.2k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.7 years ago mbenegas • 0
2
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3
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1.5k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 2.3 years ago by 41k • written 2.3 years ago by • 0
2
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6
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769
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
2
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2
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1.9k
views
Normal Patient Samples from GSE62944
GSE62944 annotationhub differentialexpression
updated 8.1 years ago by ▴ 390 • written 8.1 years ago by • 0
2
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3
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911
views
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
2.2 years ago nhaus ▴ 30
2
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8
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2.1k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.0 years ago • updated 2.9 years ago Jane ▴ 10
2
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2
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1.3k
views
Why does limma want log2 intensities but DESeq2 use raw counts?
limma DifferentialExpression DESeq2
3.0 years ago tjbencomo • 0
2
votes
2
replies
6.8k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 2.6 years ago by ★ 4.1k • written 2.6 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
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Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
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