Showing : Deseq2 • reset
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 23 hours ago by 66k • written 2 days ago by ▴ 720
2
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4
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192
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 1 day ago by 42k • written 4 days ago by • 0
0
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6
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562
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
4 days ago • updated 1 day ago Ken C • 0
4
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9
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292
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 5 days ago by ★ 4.1k • written 6 days ago by • 0
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3
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141
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 6 days ago by 42k • written 7 days ago by • 0
1
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2
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262
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
7 days ago • updated 5 days ago BioinfGuru ▴ 30
0
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8
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537
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 6 days ago by ▴ 30 • written 8 days ago by • 0
0
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1
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108
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 7 days ago by 42k • written 8 days ago by • 0
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1
reply
188
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
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1
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116
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 12 days ago by ★ 4.1k • written 12 days ago by • 0
2
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7
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429
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
13 days ago • updated 10 days ago sajadahmad41454 • 0
2
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3
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264
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 16 days ago by ★ 4.1k • written 18 days ago by • 0
1
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1
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196
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Handling multiple differential expression comparisons
DESeq2
updated 16 days ago by 42k • written 18 days ago by ▴ 10
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6
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309
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 17 days ago by ★ 1.4k • written 18 days ago by ▴ 130
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2
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175
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DESeq2 v1.35.0
DESeq2
updated 19 days ago by 42k • written 19 days ago by • 0
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2
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219
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Deseq2 and Normalization of RNA sequencing data
DESeq2
19 days ago • updated 18 days ago kcarey • 0
0
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3
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230
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 days ago by ★ 4.1k • written 19 days ago by • 0
1
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3
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310
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 13 days ago by ★ 4.1k • written 19 days ago by • 0
0
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3
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305
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 19 days ago by 42k • written 20 days ago by • 0
1
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1
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161
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
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1
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141
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putting my own expression data in deseq2
DESeq2
updated 21 days ago by ★ 4.1k • written 21 days ago by • 0
0
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2
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173
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
21 days ago • updated 18 days ago Aurora • 0
0
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1
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141
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
3
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3
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275
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 22 days ago by ★ 4.1k • written 22 days ago by ▴ 10
1
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3
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258
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 25 days ago by 42k • written 25 days ago by • 0
2
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9
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430
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 25 days ago by 66k • written 26 days ago by • 0
0
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2
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230
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PCA plot suggestions
DESeq2 PCAtools
updated 25 days ago by 42k • written 26 days ago by • 0
0
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1
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168
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 26 days ago by 42k • written 27 days ago by • 0
1
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3
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240
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Different Shrunk Log2FC according with reference
DESeq2
updated 27 days ago by 42k • written 27 days ago by ▴ 20
1
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4
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362
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
27 days ago • updated 25 days ago winwater0928 • 0
3
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1
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330
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 27 days ago by 42k • written 28 days ago by ▴ 40
0
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8
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401
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 26 days ago by ★ 1.4k • written 28 days ago by • 0
3
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3
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254
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 28 days ago by 42k • written 29 days ago by • 0
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1
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160
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rlog transformation
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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1
reply
132
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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4
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272
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
4 weeks ago lonn • 0
1
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2
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758
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 25 days ago Patadù ▴ 10
0
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1
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171
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 4 weeks ago by ★ 4.1k • written 4 weeks ago by • 0
0
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1
reply
151
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covariate with negative and positive values
DESeq2
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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3
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235
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 20
0
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4
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294
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DEG with low counts
DESeq2
updated 4 weeks ago by 42k • written 5 weeks ago by • 0
0
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1
reply
153
views
Deseq2 Rlog transformation
DESeq2
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
1
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2
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217
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Design Matrix within group comparison more than two groups
DESeq2
5 weeks ago hemantcnaik • 0
0
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1
reply
155
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Bioinformatics student
Des DESeq2
updated 5 weeks ago by • 0 • written 5 weeks ago by • 0
0
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1
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202
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DESeq2 gives an error and R crashes
DESeq2
5 weeks ago Shefali • 0
1
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2
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268
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How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 4 weeks ago Weiqian ▴ 10
0
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1
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195
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
0
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2
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184
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 6 weeks ago by 66k • written 6 weeks ago by • 0
0
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2
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250
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 5 weeks ago by 42k • written 6 weeks ago by ▴ 30
0
votes
2
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267
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Regressing out batch effects
DESeq2
updated 5 weeks ago by 42k • written 6 weeks ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue by shepherl 3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq? by baptiste.bidon • 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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