Showing : DESeq2 • reset
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Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
6 hours ago bhandary.8590 ▴ 20
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116
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DESeq2 - Comparing Comparisons
DESeq2
updated 2 days ago by 67k • written 2 days ago by • 0
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4
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279
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lfcShrink and alpha value
lfcShrink DESeq2
7 days ago • updated 2 days ago cropero • 0
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168
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DESeq2- merging technical vs biological replicates
DESeq2 RNASeqData
updated 4 days ago by 43k • written 11 days ago by • 0
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106
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DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates DESeq2
updated 4 days ago by 43k • written 4 days ago by • 0
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156
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
10 days ago • updated 9 days ago Anna • 0
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2
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453
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Deseq2 res Function
DESeq2
updated 11 days ago by 67k • written 13 days ago by ▴ 10
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348
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
14 days ago NB • 0
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5
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325
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Identical samples after deseq2 batch effect removal
DESeq2
updated 14 days ago by 43k • written 15 days ago by • 0
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192
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 15 days ago by 67k • written 15 days ago by • 0
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244
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
16 days ago • updated 15 days ago Denise • 0
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115
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eRNAs count
RNASeq DESeq2
updated 18 days ago by ★ 4.6k • written 18 days ago by • 0
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369
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DESeq2 rerun returns different results
DESeq2
updated 21 days ago by ★ 4.6k • written 21 days ago by • 0
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1
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201
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 22 days ago by 43k • written 23 days ago by • 0
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168
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DESeq2 "Not full rank" and "less than full rank" error
DESeq2 deseq
updated 24 days ago by ★ 4.1k • written 24 days ago by • 0
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553
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Handling biological replicates in DESeq2
DESeq2
updated 24 days ago by ★ 4.6k • written 25 days ago by • 0
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25k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.9 years ago by ▴ 30
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6
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907
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Volcano plot has many values around zero
RNA-seq DESeq2 volcanoplot
updated 28 days ago by 43k • written 28 days ago by ▴ 10
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344
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DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 4 weeks ago by • 0
4
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5
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598
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DESeq Input from Salmon + tximport/tximeta
tximportData summarizeToGene tximport DESeq2 salmon
4 weeks ago LuciaNhu • 0
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1
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374
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Average expression of genes across replicates
DESeq2
updated 4 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
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News: RNAseq data analysis with R/Bioconductor (4-15 November)
DESeq2 GenomicRanges
5 weeks ago info ▴ 10
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1.3k
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Question about using LRT test for time course experiments with DESeq2
DESeq2
5 weeks ago • updated 4 weeks ago Denise • 0
0
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1
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323
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Deseq to output continous sequencing data
DESeq2
updated 5 weeks ago by 43k • written 8 weeks ago by • 0
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4
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778
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Adjusted p-values become NA when sub-setting samples
DESeq2
8 weeks ago • updated 4 weeks ago txema.heredia • 0
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861
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Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 5 weeks ago by • 0
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2
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334
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ESTMATE, MCPcounter, EPIC, xCell input
DESeq2 ESTIMATE RNASeqData MCPcounter
written 6 weeks ago by • 0
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1
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277
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Should zero counts in some replicates lead to inflated p-values?
DESeq2
updated 6 weeks ago by 43k • written 6 weeks ago by • 0
2
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3
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1.0k
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Analysis of large RNA-Seq Datasets
DESeq2
updated 6 weeks ago by 43k • written 7 weeks ago by • 0
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4
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734
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DESeq2 - interactions when using factors concatenated into group
DESeq2
7 weeks ago • updated 6 weeks ago boczniak767 ▴ 740
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190
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2 factor analysis using DESeq2 but the result is not what I expected from the design
DESeq2
7 weeks ago JY • 0
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1
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273
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How does deseq2 address intra group variance when calculating log2foldchange
DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
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2
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200
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how to extract expression matrix post deseq2
DESeq2
written 7 weeks ago by • 0
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2
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202
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Using Normalized Counts in DESeq2
DESeq2
updated 7 weeks ago by 43k • written 7 weeks ago by • 0
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2
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245
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When running contrasts, does it use normalized read counts?
DESeq2
7 weeks ago Katherine • 0
0
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1
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201
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How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 7 weeks ago by ★ 1.4k • written 8 weeks ago by • 0
3
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4
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481
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Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
8 weeks ago Eva ▴ 10
1
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4
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485
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Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
updated 7 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
0
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1
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176
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 8 weeks ago by 43k • written 8 weeks ago by • 0
3
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11
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725
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Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 8 weeks ago by • 0
2
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4
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407
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RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
8 weeks ago jihoon.kim.1495 ▴ 10
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6
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812
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 5 weeks ago by 43k • written 8 weeks ago by • 0
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4
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446
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How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 8 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
0
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2
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280
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RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
9 weeks ago • updated 8 weeks ago paul.meraner • 0
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0
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189
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News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
8 weeks ago • updated 5 weeks ago info ▴ 10
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5
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592
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heatmap with batch effect
DESeq2 BatchEffect
9 weeks ago • updated 8 weeks ago tothuhien • 0
0
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2
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363
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How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
1
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1
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276
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Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 9 weeks ago by 67k • written 9 weeks ago by • 0
1
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1
reply
239
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Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
1
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1
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331
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DEseq 2 LFC shrinkage with apeglm in single-cell pseudobulk: strange volcano plot results
DESeq2
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by • 0
50 results • Page 1 of 1
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Comment: sva: get a sv for RIN scores by gabriel.hoffman ▴ 170
Agreed. I'll add that with small sample size, a covariate can explain some fraction of expression variation even under the null.
Comment: RSubread output significantly different from bash Subread output by Aimee • 0
Thank you! I will try rerunning with that parameter and see if it fixes the discrepancy! I'll report back. Update: This completely resolve…
Answer: RSubread output significantly different from bash Subread output by ATpoint ★ 4.6k
The R version counts multimappers (countMultiMappingReads is TRUE by default) while the command line version does not. It's beyond me why t…
Comment: Can't post a question? by Aimee • 0
I copied my text to a file in linux and ran: ```r grep --color='auto' -P -n "[^\x00-\x7F]" filename.txt ``` It highlighted everything that…
Answer: sva: get a sv for RIN scores by Gordon Smyth 52k
Surrogate variables are not constructed from known variates, so one doesn't get surrogate variables for RIN scores. I am guessing that the …
Votes
Answer: RSubread output significantly different from bash Subread output
Answer: RSubread output significantly different from bash Subread output
Answer: How to annotate a limma Elist raw class object with an annotation file
Comment: How to annotate a limma Elist raw class object with an annotation file
QSEA- Extraction of Normalized methylation across the samples
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