Showing : deseq2 • reset
6
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19
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2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 22 days ago by • 0 • written 4.6 years ago by ▴ 10
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2 SpikeIn Normalization
updated 12 days ago by • 0 • written 16 months ago by ▴ 10
1
vote
2
replies
763
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
5 weeks ago • updated 26 days ago Patadù ▴ 10
0
votes
6
replies
584
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
5 days ago • updated 2 days ago Ken C • 0
0
votes
8
replies
544
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2 pcaExplorer
updated 7 days ago by ▴ 30 • written 9 days ago by • 0
1
vote
4
replies
536
views
DEseq2 coefficient
DESeq2 coefficient
12 weeks ago • updated 21 days ago JKim • 0
2
votes
7
replies
436
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
14 days ago • updated 11 days ago sajadahmad41454 • 0
2
votes
9
replies
433
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 27 days ago by 66k • written 27 days ago by • 0
0
votes
8
replies
404
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 27 days ago by ★ 1.4k • written 29 days ago by • 0
1
vote
4
replies
364
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
28 days ago • updated 26 days ago winwater0928 • 0
3
votes
1
reply
331
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 28 days ago by 42k • written 29 days ago by ▴ 40
1
vote
3
replies
316
views
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 21 days ago by • 0
0
votes
3
replies
309
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 20 days ago by 42k • written 21 days ago by • 0
0
votes
6
replies
309
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 18 days ago by ★ 1.4k • written 19 days ago by ▴ 130
4
votes
9
replies
303
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2 timecoursedata GeneExpression
updated 6 days ago by ★ 4.1k • written 7 days ago by • 0
3
votes
3
replies
276
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 23 days ago by ★ 4.1k • written 23 days ago by ▴ 10
2
votes
3
replies
265
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 17 days ago by ★ 4.1k • written 19 days ago by • 0
1
vote
2
replies
265
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2 eigencorplot PCAtools
8 days ago • updated 6 days ago BioinfGuru ▴ 30
1
vote
3
replies
260
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 26 days ago by 42k • written 27 days ago by • 0
3
votes
3
replies
257
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 29 days ago by 42k • written 4 weeks ago by • 0
1
vote
3
replies
242
views
Different Shrunk Log2FC according with reference
DESeq2
updated 28 days ago by 42k • written 28 days ago by ▴ 20
0
votes
3
replies
234
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 20 days ago by ★ 4.1k • written 20 days ago by • 0
0
votes
2
replies
230
views
PCA plot suggestions
DESeq2 PCAtools
updated 26 days ago by 42k • written 27 days ago by • 0
0
votes
2
replies
219
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
20 days ago • updated 19 days ago kcarey • 0
2
votes
4
replies
202
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 2 days ago by 42k • written 5 days ago by • 0
1
vote
1
reply
197
views
Handling multiple differential expression comparisons
DESeq2
updated 17 days ago by 42k • written 19 days ago by ▴ 10
0
votes
1
reply
190
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 12 days ago by ★ 4.1k • written 12 days ago by • 0
0
votes
2
replies
176
views
DESeq2 v1.35.0
DESeq2
updated 20 days ago by 42k • written 20 days ago by • 0
0
votes
2
replies
174
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
22 days ago • updated 19 days ago Aurora • 0
0
votes
1
reply
168
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 27 days ago by 42k • written 28 days ago by • 0
1
vote
1
reply
161
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 22 days ago by 42k • written 22 days ago by • 0
0
votes
3
replies
147
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 7 days ago by 42k • written 8 days ago by • 0
0
votes
1
reply
142
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 22 days ago by 42k • written 23 days ago by • 0
0
votes
1
reply
141
views
putting my own expression data in deseq2
DESeq2
updated 22 days ago by ★ 4.1k • written 22 days ago by • 0
1
vote
3
replies
123
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 2 days ago by 66k • written 3 days ago by ▴ 720
0
votes
1
reply
116
views
normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 13 days ago by ★ 4.1k • written 13 days ago by • 0
0
votes
1
reply
115
views
normalization across different species for DESeq2 analysis
DESeq2 normalization Normalization acrossspecies
updated 8 days ago by 42k • written 9 days ago by • 0
0
votes
7
replies
85
views
Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
updated 3 hours ago by 42k • written 7 hours ago by ▴ 720
38 results • Page 1 of 1
Recent ...
Replies
Answer: Help with infinite recursion - non-zero exit status in installation of GenomeInf by James W. MacDonald 66k
Maybe just try again? ``` > install("GenomeInfoDbData", force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositorie…
Comment: Help with infinite recursion - non-zero exit status in installation of GenomeInf by Brandon • 0
Hello, As an update, I am able to install and load GenomeInfoDb successfully in a fresh renv in my WSL distro. However, I'm not sure what …
Comment: slingshot: error with plot3d.SlingshotDataSet by Kelly Street • 0
This issue has been addressed [on GitHub][1]. [1]: https://github.com/kstreet13/slingshot/issues/249
Comment: Slightly different count plots from R and spreadsheet by Michael Love 42k
Change timepoint to an integer in the data frame: ``` as.numeric(as.character( <factor> )) ``` Then it should make points instead of boxe…
Answer: WGNCA kME vs. kIM by Vitor • 0
You can compare kIM and kME within module assignments. The plot below is for my network (I used Pearson correlation and signed network). !…
Votes
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
DESeq2 DE gene expression of scRNA-seq pseudobulk
Answer: Multiple factor DSEq2 result generates weird volcano plot
DESeq2 for single cell pseudobulk processing
Simultaneously adding two different covariates in the model gives error in DESeq2.
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