Showing : DEseq2 • reset
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Plot PCA with ellipses using ggplot
DESeq2 ggplot PCA
4 hours ago robledoj13 • 0
3
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5
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268
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A question occur when using DESeq2 on a complex design
DESeq2 rnaseqGene RNASeq
1 day ago MedocRafael • 0
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DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2 RNAseq
8 days ago • updated 1 day ago mila ▴ 10
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150
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DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2 volcanoplot LRT
2 days ago Eric • 0
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3
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273
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 3 days ago by ★ 4.2k • written 3 days ago by • 0
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3
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300
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Doubt about model in paired samples (intercept ?)
DESeq2
updated 4 days ago by 42k • written 6 days ago by • 0
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10
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622
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Two treatments, one control
DESeq2 stageR
16 days ago • updated 4 days ago alephreish • 0
3
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8
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24k
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Deseq: What does "BaseMean" mean?
deseq2
written 5.9 years ago by • 0
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2
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730
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How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
7 days ago • updated 4 days ago Fiona • 0
2
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3
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260
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DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2 R
written 8 days ago by • 0
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1
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117
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 8 days ago by ★ 4.2k • written 8 days ago by • 0
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116
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DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering DESeq2 outliers
9 days ago smac_head • 0
4
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12
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528
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DGE with a Continuous Variable
DESeq2 model
updated 14 hours ago by 42k • written 10 days ago by • 0
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321
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DESeq2: two conditions two genotypes
DESeq2
15 days ago • updated 12 days ago Rocio • 0
2
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3
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376
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DESeq normalized counts vs CQN and statistics
DESeq2 cqn
updated 11 days ago by 42k • written 15 days ago by • 0
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212
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Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn RUVSeq DESeq2 RUV
updated 15 days ago by 42k • written 19 days ago by • 0
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1
reply
149
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unreal negative log2fc values
DESeq2 des
updated 21 days ago by 66k • written 21 days ago by • 0
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153
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What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables DESeq2 BatchEffect bulkrna-seq sva-seq
23 days ago • updated 22 days ago BioinfGuru ▴ 30
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1
reply
224
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LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 23 days ago by 42k • written 24 days ago by • 0
1
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8
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481
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Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 18 days ago by 51k • written 4 weeks ago by • 0
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2
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1.1k
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Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
4 weeks ago sropri • 0
0
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1
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172
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Deseq2 design matrix
DESeq2 Designmatrix limma
updated 4 weeks ago by 66k • written 4 weeks ago by • 0
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1
reply
188
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DESeq2 - vst() - log2FC - no replicates
DESeq2 log2FC vst()
updated 5 weeks ago by ★ 4.2k • written 5 weeks ago by • 0
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5
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385
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DESeq2 ML Query
DESeq2
updated 10 days ago by 42k • written 5 weeks ago by • 0
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2
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256
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Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression DESeq2
updated 5 weeks ago by 66k • written 5 weeks ago by • 0
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1
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211
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Significant genes in DESeq2 analysis
DESeq2 RNASeq
updated 5 weeks ago by 66k • written 5 weeks ago by • 0
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3
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331
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Combining two bulk RNA seq datasets
RNASeqData DESeq2 Normalization
5 weeks ago Tanvi • 0
0
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1
reply
960
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In a 3 group DEG analysis with three batches, can I use 1 group in all three batches to correct for the batch effect?
DESeq2
updated 6 weeks ago by 42k • written 7 weeks ago by • 0
2
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1
reply
323
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Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 6 weeks ago by 42k • written 7 weeks ago by ▴ 10
2
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1
reply
233
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 6 weeks ago by 66k • written 6 weeks ago by ▴ 50
1
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9
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607
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 5 weeks ago by 66k • written 6 weeks ago by • 0
1
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3
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332
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 6 weeks ago by 66k • written 6 weeks ago by ▴ 50
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6
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1.9k
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Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 6 weeks ago by ★ 4.2k • written 15 months ago by ▴ 20
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2
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220
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Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
6 weeks ago BioinfGuru ▴ 30
1
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2
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421
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Cohen's D calculation for differentially expressed genes via DESeq2 results summary stats
DESeq2
7 weeks ago a_p • 0
0
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1
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193
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Can we compare 3 different experimental conditions with DESeq2?
DESeq2 StatisticalMethod
updated 7 weeks ago by ★ 1.4k • written 7 weeks ago by • 0
0
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1
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198
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How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 7 weeks ago by 66k • written 7 weeks ago by • 0
1
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2
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2.0k
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using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 7 weeks ago by ▴ 40 • written 4.7 years ago by • 0
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1
reply
218
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multiple condition issue running DESeq
DESeq2
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
0
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3
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326
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Ploting of normalized counts after batch removal
DESeq2
updated 7 weeks ago by 51k • written 7 weeks ago by ▴ 10
1
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1
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198
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makeExampleDESeqDataSet using pilot data
DESeq2
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
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2
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240
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Best way to describe DEseq2 design
DESeq2
updated 8 weeks ago by ★ 1.4k • written 8 weeks ago by • 0
1
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2
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271
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Deseq2
DESeq2 rnaseqGene
updated 8 weeks ago by ▴ 210 • written 8 weeks ago by • 0
1
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1
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225
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LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 8 weeks ago by 66k • written 8 weeks ago by ▴ 740
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6
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459
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Counter-directional LFC shrinkage
DESeq2
updated 8 weeks ago by 42k • written 8 weeks ago by • 0
0
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2
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300
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 8 weeks ago by ★ 4.0k • written 8 weeks ago by • 0
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3
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367
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GSVA function
DESeq2 GSVA ssGSEA
updated 8 weeks ago by ★ 3.3k • written 9 weeks ago by • 0
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2
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300
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
9 weeks ago • updated 8 weeks ago sukeshinik5 • 0
0
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4
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554
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 8 weeks ago by ★ 4.2k • written 9 weeks ago by • 0
1
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8
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423
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
9 weeks ago boczniak767 ▴ 740
50 results • Page 1 of 1
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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