Showing : deseq2 • reset
6
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19
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2.5k
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DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 7 days ago by • 0 • written 4.6 years ago by ▴ 10
9
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12
replies
7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 19 days ago by • 0 • written 8.8 years ago by ▴ 30
2
votes
9
replies
394
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 12 days ago by 65k • written 12 days ago by • 0
0
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8
replies
356
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 12 days ago by ★ 1.3k • written 14 days ago by • 0
0
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7
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424
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DESeq filtering specific to contrasts
DESeq2
updated 18 days ago by 42k • written 11 weeks ago by • 0
0
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6
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221
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 3 days ago by ★ 1.3k • written 5 days ago by ▴ 130
2
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5
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1.2k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 20 days ago by • 0 • written 10 months ago by • 0
2
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5
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757
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DESeq2 setting significant p-value
DESeq2
updated 18 days ago by 42k • written 5.0 years ago by ▴ 10
1
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4
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483
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DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 6 days ago JKim • 0
0
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4
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241
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
20 days ago • updated 17 days ago lonn • 0
1
vote
4
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335
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
13 days ago • updated 11 days ago winwater0928 • 0
0
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4
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270
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DEG with low counts
DESeq2
updated 18 days ago by 42k • written 23 days ago by • 0
0
votes
4
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603
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 21 days ago by 42k • written 6 months ago by • 0
3
votes
3
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231
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 14 days ago by 42k • written 15 days ago by • 0
1
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3
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216
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Different Shrunk Log2FC according with reference
DESeq2
updated 13 days ago by 42k • written 13 days ago by ▴ 20
0
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3
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256
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 6 days ago by 42k • written 7 days ago by • 0
3
votes
3
replies
241
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 8 days ago by ★ 4.1k • written 8 days ago by ▴ 10
0
votes
3
replies
207
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 21 days ago by 42k • written 22 days ago by ▴ 20
1
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3
replies
227
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 11 days ago by 42k • written 12 days ago by • 0
2
votes
3
replies
182
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 2 days ago by ★ 4.1k • written 4 days ago by • 0
0
votes
3
replies
151
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 5 days ago by ★ 4.1k • written 6 days ago by • 0
0
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2
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112
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DESeq2 v1.35.0
DESeq2
updated 5 days ago by 42k • written 5 days ago by • 0
1
vote
2
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245
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How to retrieve detailed regression results from deseq2
DESeq2
27 days ago • updated 18 days ago Weiqian ▴ 10
1
vote
2
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718
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
20 days ago • updated 11 days ago ussarizona ▴ 10
0
votes
2
replies
249
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Regressing out batch effects
DESeq2
updated 28 days ago by 42k • written 4 weeks ago by • 0
0
votes
2
replies
214
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PCA plot suggestions
DESeq2 PCAtools
updated 11 days ago by 42k • written 12 days ago by • 0
1
vote
2
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199
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Design Matrix within group comparison more than two groups
DESeq2
25 days ago • updated 24 days ago hemantcnaik • 0
0
votes
2
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128
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
7 days ago • updated 4 days ago Aurora • 0
0
votes
2
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223
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 28 days ago by 42k • written 4 weeks ago by ▴ 30
1
vote
2
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165
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Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
6 days ago • updated 1 hour ago angelathuynh5 • 0
0
votes
2
replies
149
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Deseq2 and Normalization of RNA sequencing data
DESeq2
6 days ago • updated 5 days ago kcarey • 0
1
vote
1
reply
107
views
Handling multiple differential expression comparisons
DESeq2
updated 2 days ago by 42k • written 4 days ago by ▴ 10
0
votes
1
reply
150
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 19 days ago by ★ 4.1k • written 20 days ago by • 0
0
votes
1
reply
133
views
Deseq2 Rlog transformation
DESeq2
updated 22 days ago by ★ 4.1k • written 23 days ago by • 0
0
votes
1
reply
167
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 28 days ago by 42k • written 28 days ago by • 0
0
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1
reply
178
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DESeq2 gives an error and R crashes
DESeq2
27 days ago • updated 26 days ago Shefali • 0
0
votes
1
reply
109
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 7 days ago by 42k • written 8 days ago by • 0
0
votes
1
reply
135
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covariate with negative and positive values
DESeq2
updated 19 days ago by 42k • written 21 days ago by • 0
0
votes
1
reply
113
views
putting my own expression data in deseq2
DESeq2
updated 7 days ago by ★ 4.1k • written 7 days ago by • 0
3
votes
1
reply
316
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 13 days ago by 42k • written 14 days ago by ▴ 40
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 19 days ago by 42k • written 19 days ago by • 0
0
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1
reply
155
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 13 days ago by 42k • written 13 days ago by • 0
1
vote
1
reply
116
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 7 days ago by 42k • written 7 days ago by • 0
0
votes
1
reply
113
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 19 days ago by 42k • written 19 days ago by • 0
0
votes
1
reply
137
views
Bioinformatics student
Des DESeq2
updated 25 days ago by • 0 • written 25 days ago by • 0
45 results • Page 1 of 1
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Replies
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by angelathuynh5 • 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by Gordon Smyth 50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Method to find pathways different between 2 groups by Gordon Smyth 50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu by James W. MacDonald 65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
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