Showing : DESeq2 • reset
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DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
updated 13 hours ago by 68k • written 18 hours ago by • 0
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4
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362
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Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 3 days ago by • 0
0
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1
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392
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Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 6 days ago by 68k • written 6 days ago by • 0
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[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
9 days ago • updated 8 days ago Luca • 0
0
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2
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370
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Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 3 days ago by 43k • written 11 days ago by ▴ 20
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911
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Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 1 day ago by • 0 • written 15 days ago by • 0
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1
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174
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DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 14 days ago by 43k • written 15 days ago by • 0
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3
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596
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how many significant figures are there in DESeq2 output
DESeq2
updated 18 days ago by ★ 4.7k • written 20 days ago by ▴ 180
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5
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980
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Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
22 days ago • updated 21 days ago picasa1983 • 0
3
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Vertical line at A=0, nothing else, on MA plot
deseq2
updated 21 days ago by ▴ 10 • written 6.0 years ago by ▴ 20
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1
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323
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How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData DESeq2 pseudobulk sing
updated 23 days ago by 68k • written 23 days ago by • 0
1
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1
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451
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Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 24 days ago by ★ 1.4k • written 24 days ago by ▴ 10
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1
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283
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DEseq2 design for additive treatment
DESeq2
updated 24 days ago by ★ 4.7k • written 25 days ago by • 0
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505
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Plot title for PCA in DESeq2
DESeq2
27 days ago • updated 23 days ago AL • 0
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3
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545
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 27 days ago by 43k • written 4 weeks ago by • 0
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Weird p-values using DESeq2?
DESeq2 RNASeq
updated 4 weeks ago by ★ 4.7k • written 4 weeks ago by • 0
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1
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155
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 5 weeks ago by 43k • written 6 weeks ago by • 0
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3
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516
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DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 5 weeks ago by • 0 • written 6 weeks ago by • 0
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2
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380
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accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 5 weeks ago by • 0 • written 6 weeks ago by • 0
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3
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447
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displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 23 days ago by • 0 • written 6 weeks ago by • 0
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3
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414
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How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 6 weeks ago by • 0 • written 7 weeks ago by ▴ 10
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1
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227
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
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2
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475
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Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 7 weeks ago by ★ 1.4k • written 7 weeks ago by • 0
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4
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972
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Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
7 weeks ago Quang NN ▴ 10
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2
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542
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How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
8 weeks ago • updated 7 weeks ago Blandine • 0
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5
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356
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 8 weeks ago by • 0
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4
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521
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
8 weeks ago Quang NN ▴ 10
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5
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426
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Differential variability modelling with vst() expression
limma DESeq2
written 10 weeks ago by • 0
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3
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569
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 10 weeks ago by • 0
2
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9
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1.0k
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
10 weeks ago • updated 8 weeks ago Quang NN ▴ 10
1
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1
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451
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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1
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217
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 10 weeks ago by ★ 1.4k • written 10 weeks ago by • 0
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1
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411
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Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 10 weeks ago by 43k • written 12 weeks ago by • 0
2
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1
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412
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 10 weeks ago by 43k • written 12 weeks ago by • 0
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2
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406
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
11 weeks ago Kucsera • 0
1
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1
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422
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
1
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9
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967
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 3 months ago by ▴ 30
4
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2
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528
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 3 months ago by ★ 4.7k • written 3 months ago by ▴ 10
1
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5
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673
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Deseq2 Design
RNASeq DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
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5
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680
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p value is 0, padj is 0
DESeq2
3 months ago Wirayatida • 0
1
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654
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
3 months ago georgii.vdovin • 0
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7
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995
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 3 months ago by • 0 • written 3 months ago by • 0
0
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1
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375
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 3 months ago by 43k • written 3 months ago by ▴ 20
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3
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512
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DESeq2 - Comparing Comparisons
DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
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4
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647
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lfcShrink and alpha value
lfcShrink DESeq2
3 months ago cropero • 0
2
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1
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411
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 3 months ago by 43k • written 3 months ago by • 0
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2
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288
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
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2
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328
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
3 months ago Anna • 0
1
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2
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632
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Deseq2 res Function
DESeq2
updated 3 months ago by 68k • written 3 months ago by ▴ 10
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4
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537
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
3 months ago NB • 0
50 results • Page 1 of 1
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Comment: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k
The covariate is accounted for when you fit the model, so you don't need to do anything with it at the contrast step. You don't need a con…
Comment: DESEQ2 looking at main effects while controlling for a continuous variable by Lennie • 0
Thank you so much for taking the time and for the detailed explanation! I was wondering, in your numeric contrast of c(1, -1, 0,0,0), doe…
Answer: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k
If you use a factor effects model (with an intercept), then you will have a baseline group (the intercept), and all other coefficients exce…
Comment: Issue with DECIPHER::IdTaxa by Daniel • 0
The issue is still there and it is a real pain. ape and ade4 are used by packages like Phyloseq. There should be a way to avoid these inc…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Gordon Smyth 52k
I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
Votes
Answer: DESEQ2 looking at main effects while controlling for a continuous variable
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
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