Showing : desEQ2 • reset
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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 2 days ago by 42k • written 9 days ago by • 0
2
votes
1
reply
149
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Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 2 days ago by 42k • written 8 days ago by ▴ 10
2
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1
reply
91
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 2 days ago by 66k • written 2 days ago by ▴ 50
1
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7
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188
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Most enriched pathway is not expressed when modifying universe parameter
DESeq2 clusterProfiler Pathways RNASeq org.Mm.eg.db
updated 1 day ago by 66k • written 4 days ago by • 0
1
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3
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180
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 4 days ago by 66k • written 4 days ago by ▴ 50
3
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6
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1.7k
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Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 4 days ago by ★ 4.2k • written 14 months ago by ▴ 20
2
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2
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113
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Double normalising when using sva and deseq2
DESeq2 Normalisation Bulkrnaseq Svaseq
6 days ago BioinfGuru ▴ 30
1
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2
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306
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Cohen's D calculation for differentially expressed genes via DESeq2 results summary stats
DESeq2
10 days ago • updated 9 days ago a_p • 0
0
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1
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113
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Can we compare 3 different experimental conditions with DESeq2?
DESeq2 StatisticalMethod
updated 8 days ago by ★ 1.4k • written 9 days ago by • 0
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1
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123
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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 9 days ago by 66k • written 10 days ago by • 0
1
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2
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1.9k
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using tximport with STAR transcript-quantification output
tximport deseq2 STAR
updated 10 days ago by ▴ 40 • written 4.6 years ago by • 0
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1
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134
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multiple condition issue running DESeq
DESeq2
updated 12 days ago by 42k • written 12 days ago by • 0
0
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3
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233
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Ploting of normalized counts after batch removal
DESeq2
updated 13 days ago by 51k • written 14 days ago by ▴ 10
1
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1
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136
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makeExampleDESeqDataSet using pilot data
DESeq2
updated 16 days ago by 42k • written 16 days ago by • 0
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2
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172
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Best way to describe DEseq2 design
DESeq2
updated 16 days ago by ★ 1.4k • written 17 days ago by • 0
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2
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196
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Deseq2
DESeq2 rnaseqGene
updated 16 days ago by ▴ 210 • written 17 days ago by • 0
1
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1
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156
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LRT, pairwise comparisons and p-value adjustment
DESeq2
updated 18 days ago by 66k • written 18 days ago by ▴ 740
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6
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341
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Counter-directional LFC shrinkage
DESeq2
updated 17 days ago by 42k • written 19 days ago by • 0
0
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2
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216
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How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat DESeq2 single-cell scRNA Pseudobulk
updated 20 days ago by ★ 4.0k • written 21 days ago by • 0
0
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3
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242
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GSVA function
DESeq2 GSVA ssGSEA
updated 20 days ago by ★ 3.3k • written 23 days ago by • 0
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2
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194
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Normalisation using clinical traits in RNA seq using DESeq2
DESeq2 clinicaltraits Normalization batchnormalisation
23 days ago • updated 20 days ago sukeshinik5 • 0
0
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4
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383
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Volcano plot of scRNA-seq data not "centered"
DESeq2
updated 21 days ago by ★ 4.2k • written 23 days ago by • 0
1
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8
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300
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Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
25 days ago • updated 24 days ago boczniak767 ▴ 740
1
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3
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242
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LRT, more than two conditions and pairwise comparisons
DESeq2
updated 26 days ago by 66k • written 27 days ago by ▴ 740
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6
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688
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
4 weeks ago • updated 27 days ago Ken C • 0
2
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4
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300
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 26 days ago by 42k • written 4 weeks ago by • 0
4
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9
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395
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Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 4 weeks ago by ★ 4.2k • written 4 weeks ago by • 0
0
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3
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199
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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1
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156
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normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
0
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9
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798
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Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 13 days ago by ▴ 30 • written 4 weeks ago by • 0
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2
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314
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How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
4 weeks ago BioinfGuru ▴ 30
0
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1
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233
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 5 weeks ago by ★ 4.2k • written 5 weeks ago by • 0
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1
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159
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 5 weeks ago by ★ 4.2k • written 5 weeks ago by • 0
2
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7
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550
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
5 weeks ago sajadahmad41454 • 0
2
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1
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279
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Handling multiple differential expression comparisons
DESeq2
6 weeks ago • updated 3 days ago Zainab ▴ 10
0
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6
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369
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 6 weeks ago by ★ 1.4k • written 6 weeks ago by ▴ 130
2
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3
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336
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
0
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2
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212
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DESeq2 v1.35.0
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
0
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2
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264
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Deseq2 and Normalization of RNA sequencing data
DESeq2
6 weeks ago kcarey • 0
0
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3
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301
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
1
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3
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394
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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 5 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
0
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3
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337
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
1
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1
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200
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
0
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2
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210
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
6 weeks ago Aurora • 0
0
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1
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158
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
0
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1
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161
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putting my own expression data in deseq2
DESeq2
updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by • 0
3
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3
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310
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 6 weeks ago by ★ 4.2k • written 6 weeks ago by ▴ 10
0
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2
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261
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PCA plot suggestions
DESeq2 PCAtools
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
1
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3
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287
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 7 weeks ago by 42k • written 7 weeks ago by • 0
2
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9
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494
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 7 weeks ago by 66k • written 7 weeks ago by • 0
50 results • Page 1 of 1
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Answer: Trouble reading samplesheet in with diffbind to create dba by Anthony • 0
I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter by adripel • 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Votes
Answer: How to do DESeq2 on Kallisto Data
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
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