Showing : DESeq2 • reset
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
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
762
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 25 days ago Patadù ▴ 10
0
votes
6
replies
574
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Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
5 days ago • updated 1 day ago Ken C • 0
0
votes
8
replies
543
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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
vote
4
replies
535
views
DEseq2 coefficient
DESeq2 coefficient
12 weeks ago • updated 20 days ago JKim • 0
2
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7
replies
435
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
14 days ago • updated 11 days ago sajadahmad41454 • 0
2
votes
9
replies
432
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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 27 days ago by • 0
0
votes
8
replies
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
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 28 days ago by ▴ 40
1
vote
3
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314
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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
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
0
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3
replies
308
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
4
votes
9
replies
302
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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 18 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 5 days ago BioinfGuru ▴ 30
1
vote
3
replies
259
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 26 days ago by 42k • written 26 days ago by • 0
3
votes
3
replies
256
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 29 days ago by 42k • written 29 days ago by • 0
1
vote
3
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242
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Different Shrunk Log2FC according with reference
DESeq2
updated 28 days ago by 42k • written 28 days ago by ▴ 20
0
votes
3
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233
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
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2
replies
230
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PCA plot suggestions
DESeq2 PCAtools
updated 25 days ago by 42k • written 27 days ago by • 0
0
votes
2
replies
219
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Deseq2 and Normalization of RNA sequencing data
DESeq2
20 days ago • updated 19 days ago kcarey • 0
2
votes
4
replies
202
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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
1
vote
1
reply
197
views
Handling multiple differential expression comparisons
DESeq2
updated 17 days ago by 42k • written 18 days ago by ▴ 10
0
votes
1
reply
189
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 19 days ago by 42k • written 19 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 27 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
146
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 7 days ago by 42k • written 7 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 22 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
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3
replies
120
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 1 day ago by 66k • written 2 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
113
views
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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3
replies
12
views
Slightly different count plots from R and spreadsheet
DESeq2 ggplot2
50 minutes ago • updated just now boczniak767 ▴ 720
38 results • Page 1 of 1
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Replies
Comment: Slightly different count plots from R and spreadsheet by ATpoint ★ 4.1k
I don't think it is the purpose of the support site to debug Excel behaviour. The issue might be how it combines replicates into a single v…
Comment: Running ENmix with mouse methylation manifest: readidat error - Error in readman by Karosham.Reddy • 0
Hi, I am having the same issues. What was the typo that you found? And were you able to solve the next problem?
Comment: recount3 problem downloading data from source sra by PABLO ANTONIO • 0
Hello Leonardo, Thanks for commenting on possible solutions. I noticed comparing your session info that I was using the previous version o…
Comment: seqlevelsStyle() not working by websterdelacruz2087055 • 0
Specify the new URL new_url <- "https://hgdownload2.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz" Use the new URL to download th…
Comment: SGSeq: moving toward diffex from SGSeq analysis by Sara • 0
Yes, thank you. I have another error now, may you please guide me. here is the code that I used till using vep: ```r # bam_path <- "~/pat…
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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