Showing : deseq2 • reset
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 1 day ago by 66k • written 2 days ago by ▴ 720
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6
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570
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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
2
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4
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198
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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
4
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9
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299
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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
0
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3
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144
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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
0
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1
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111
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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
0
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8
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541
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 7 days ago by ▴ 30 • written 8 days ago by • 0
1
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2
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265
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
8 days ago • updated 5 days ago BioinfGuru ▴ 30
0
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1
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189
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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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435
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
13 days ago • updated 10 days ago sajadahmad41454 • 0
1
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1
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197
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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 18 days ago by ★ 1.4k • written 19 days ago by ▴ 130
2
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3
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265
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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
0
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2
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176
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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
20 days ago • updated 19 days ago kcarey • 0
0
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3
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231
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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 20 days ago by • 0
1
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3
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313
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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 14 days ago by ★ 4.1k • written 20 days ago by • 0
0
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3
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308
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 20 days ago by 42k • written 21 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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2
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174
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
22 days ago • updated 18 days ago Aurora • 0
0
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1
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142
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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 22 days ago by • 0
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
3
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3
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276
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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 23 days ago by ▴ 10
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 27 days ago by • 0
1
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3
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259
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 25 days ago by 42k • written 26 days ago by • 0
2
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9
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431
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 26 days ago by 66k • 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 27 days ago by 42k • written 27 days ago by • 0
1
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3
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242
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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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363
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
28 days ago • updated 26 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 28 days ago by 42k • written 28 days ago by ▴ 40
0
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8
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404
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 27 days ago by ★ 1.4k • written 28 days ago by • 0
3
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3
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256
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 28 days ago by 42k • written 29 days ago by • 0
1
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761
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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
1
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4
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534
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DEseq2 coefficient
DESeq2 coefficient
12 weeks ago • updated 20 days ago JKim • 0
0
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2
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1.5k
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How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 11 days ago by • 0 • written 16 months ago by ▴ 10
6
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19
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2.6k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 21 days ago by • 0 • written 4.6 years ago by ▴ 10
37 results • Page 1 of 1
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Comment: slingshot: error with plot3d.SlingshotDataSet by Happiness • 0
Hi please i am encountering similar issue how did you fix it. Here is the code: ## Run Slingshot p3.neuron.sds <- slingshot(Embeddings(…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by mohammedtoufiq91 ▴ 10
https://support.bioconductor.org/u/5106/ thank you very much.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Thank you so much!
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 …
Votes
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
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