Showing : DESeq2 • reset
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
11 hours ago • updated 10 hours ago georgeyu703 • 0
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How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
2 days ago • updated 2 hours ago Quang NN ▴ 10
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Differential variability modelling with vst() expression
limma DESeq2
written 12 days ago by • 0
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DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
13 days ago • updated 11 days ago sindhuri • 0
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9
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721
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Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
14 days ago • updated 2 days ago Quang NN ▴ 10
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275
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Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 14 days ago by 43k • written 14 days ago by • 0
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152
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Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 15 days ago by ★ 1.4k • written 15 days ago by • 0
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334
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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 18 days ago by 43k • written 29 days ago by • 0
2
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1
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342
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Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 18 days ago by 43k • written 26 days ago by • 0
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258
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DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
24 days ago • updated 22 days ago Kucsera • 0
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367
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Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 4 weeks ago by 43k • written 5 weeks ago by • 0
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 5 weeks ago by ▴ 30
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Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 5 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
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Deseq2 Design
RNASeq DESeq2
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
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p value is 0, padj is 0
DESeq2
5 weeks ago Wirayatida • 0
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
5 weeks ago georgii.vdovin • 0
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7
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DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 5 weeks ago by • 0 • written 6 weeks ago by • 0
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1
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277
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 6 weeks ago by 43k • written 6 weeks ago by ▴ 20
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DESeq2 - Comparing Comparisons
DESeq2
updated 5 weeks ago by 67k • written 6 weeks ago by • 0
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535
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lfcShrink and alpha value
lfcShrink DESeq2
7 weeks ago • updated 6 weeks ago cropero • 0
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280
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 7 weeks ago by 43k • written 8 weeks ago by • 0
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
8 weeks ago • updated 7 weeks ago Anna • 0
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556
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Deseq2 res Function
DESeq2
updated 8 weeks ago by 67k • written 8 weeks ago by ▴ 10
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
8 weeks ago NB • 0
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452
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Identical samples after deseq2 batch effect removal
DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
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253
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 8 weeks ago by 67k • written 8 weeks ago by • 0
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311
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
8 weeks ago Denise • 0
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169
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eRNAs count
RNASeq DESeq2
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
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405
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DESeq2 rerun returns different results
DESeq2
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 9 weeks ago by 43k • written 10 weeks ago by • 0
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246
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 10 weeks ago by ★ 4.1k • written 10 weeks ago by • 0
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Handling biological replicates in DESeq2
DESeq2
updated 10 weeks ago by ★ 4.6k • written 10 weeks ago by • 0
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 6.0 years ago by ▴ 30
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 10 weeks ago by 43k • written 10 weeks ago by ▴ 10
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 11 weeks ago by • 0
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
11 weeks ago LuciaNhu • 0
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415
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Average expression of genes across replicates
DESeq2
updated 11 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
11 weeks ago info ▴ 10
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Question about using LRT test for time course experiments with DESeq2
DESeq2
12 weeks ago • updated 11 weeks ago Denise • 0
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1
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367
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Deseq to output continous sequencing data
DESeq2
updated 12 weeks ago by 43k • written 3 months ago by • 0
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Adjusted p-values become NA when sub-setting samples
DESeq2
3 months ago • updated 10 weeks ago txema.heredia • 0
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 12 weeks ago by • 0
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377
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 3 months ago by • 0
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
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1.1k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
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799
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DESeq2 - interactions when using factors concatenated into group
DESeq2
3 months ago • updated 12 weeks ago boczniak767 ▴ 740
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233
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
3 months ago JY • 0
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311
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
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how to extract expression matrix post deseq2
DESeq2
written 3 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by Quang NN ▴ 10
Thank you so much for taking time to provide this clarification!
Comment: How can I generate a heatmap and clustering of differentially expressed genes in by Renuka • 0
Thanks Kelvin i had same doubt .Do i need to do log2 (FPKMcounts) for this
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Michael, Thank you very much!
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
Yes, with the knowledge that, it is expected to be underpowered.
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Thank you, Michael. How? Could you provide more details? Can I just do it as usual, I mean to include batch in the model?
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