Showing : DESeq2 • reset
6
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19
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2.4k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by • 0 • written 4.6 years ago by ▴ 10
9
votes
12
replies
7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 14 days ago by • 0 • written 8.8 years ago by ▴ 30
2
votes
9
replies
345
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 7 days ago by 65k • written 7 days ago by • 0
0
votes
8
replies
325
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 8 days ago by ★ 1.3k • written 9 days ago by • 0
0
votes
7
replies
408
views
DESeq filtering specific to contrasts
DESeq2
updated 13 days ago by 41k • written 11 weeks ago by • 0
1
vote
6
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419
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 29 days ago by 41k • written 29 days ago by • 0
2
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5
replies
736
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DESeq2 setting significant p-value
DESeq2
updated 13 days ago by 41k • written 5.0 years ago by ▴ 10
2
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5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 15 days ago by • 0 • written 10 months ago by • 0
0
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4
replies
592
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 16 days ago by 41k • written 6 months ago by • 0
1
vote
4
replies
457
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DEseq2 coefficient
DESeq2 coefficient
9 weeks ago • updated 1 day ago JKim • 0
1
vote
4
replies
304
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
9 days ago • updated 7 days ago winwater0928 • 0
0
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4
replies
69
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Once again a "Model matrix not full rank"
DESeq2 design coldata
11 hours ago • updated 1 hour ago arfranco ▴ 130
0
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4
replies
230
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
15 days ago • updated 13 days ago lonn • 0
0
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4
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260
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DEG with low counts
DESeq2
updated 13 days ago by 41k • written 18 days ago by • 0
0
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3
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200
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 16 days ago by 41k • written 17 days ago by ▴ 20
1
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3
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190
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 6 days ago by 41k • written 7 days ago by • 0
0
votes
3
replies
221
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 1 day ago by 41k • written 2 days ago by • 0
1
vote
3
replies
203
views
Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by 41k • written 8 days ago by ▴ 20
0
votes
3
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95
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 21 hours ago by ★ 4.1k • written 1 day ago by • 0
3
votes
3
replies
213
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 9 days ago by 41k • written 10 days ago by • 0
3
votes
3
replies
199
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 3 days ago by ★ 4.1k • written 4 days ago by ▴ 10
0
votes
2
replies
185
views
PCA plot suggestions
DESeq2 PCAtools
updated 6 days ago by 41k • written 8 days ago by • 0
0
votes
2
replies
52
views
DESeq2 v1.35.0
DESeq2
updated 15 hours ago by 41k • written 16 hours ago by • 0
1
vote
2
replies
239
views
How to retrieve detailed regression results from deseq2
DESeq2
22 days ago • updated 13 days ago Weiqian ▴ 10
1
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2
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696
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
15 days ago • updated 6 days ago ussarizona ▴ 10
0
votes
2
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234
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Regressing out batch effects
DESeq2
updated 23 days ago by 41k • written 28 days ago by • 0
0
votes
2
replies
161
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 27 days ago by 65k • written 27 days ago by • 0
1
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2
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190
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Design Matrix within group comparison more than two groups
DESeq2
20 days ago • updated 19 days ago hemantcnaik • 0
0
votes
2
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215
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 23 days ago by 41k • written 27 days ago by ▴ 30
0
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2
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78
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Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 8 hours ago kcarey • 0
0
votes
1
reply
130
views
Bioinformatics student
Des DESeq2
updated 20 days ago by • 0 • written 20 days ago by • 0
0
votes
1
reply
126
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rlog transformation
DESeq2
updated 14 days ago by 41k • written 14 days ago by • 0
0
votes
1
reply
106
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 14 days ago by 41k • written 14 days ago by • 0
0
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1
reply
128
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Deseq2 Rlog transformation
DESeq2
updated 17 days ago by ★ 4.1k • written 19 days ago by • 0
0
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1
reply
158
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 23 days ago by 41k • written 23 days ago by • 0
0
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1
reply
139
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 14 days ago by ★ 4.1k • written 15 days ago by • 0
0
votes
1
reply
87
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
0
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1
reply
76
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 2 days ago by 41k • written 3 days ago by • 0
0
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1
reply
88
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putting my own expression data in deseq2
DESeq2
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
1
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1
reply
84
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
0
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1
reply
128
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covariate with negative and positive values
DESeq2
updated 14 days ago by 41k • written 16 days ago by • 0
0
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1
reply
173
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DESeq2 gives an error and R crashes
DESeq2
22 days ago • updated 21 days ago Shefali • 0
0
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1
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103
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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 1 day ago by ★ 4.1k • written 1 day ago by • 0
0
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1
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136
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 8 days ago by 41k • written 8 days ago by • 0
3
votes
1
reply
299
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 9 days ago by 41k • written 9 days ago by ▴ 40
1
vote
1
reply
160
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DESeq2 - Missing values in count matrix
DESeq2
updated 28 days ago by 65k • written 28 days ago by • 0
46 results • Page 1 of 1
Recent ...
Replies
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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