Showing : DESEq2 • reset
9
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 21 days ago by • 0 • written 8.8 years ago by ▴ 30
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 9 days ago by • 0 • written 4.6 years ago by ▴ 10
3
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3
replies
245
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 10 days ago by ★ 4.1k • written 11 days ago by ▴ 10
3
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3
replies
234
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 16 days ago by 42k • written 17 days ago by • 0
3
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1
reply
316
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 16 days ago by 42k • written 16 days ago by ▴ 40
2
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5
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147
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
2 days ago • updated 5 hours ago sajadahmad41454 • 0
2
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5
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768
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DESeq2 setting significant p-value
DESeq2
updated 20 days ago by 42k • written 5.0 years ago by ▴ 10
2
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9
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405
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 14 days ago by 65k • written 14 days ago by • 0
2
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3
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203
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 4 days ago by ★ 4.1k • written 6 days ago by • 0
2
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5
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1.2k
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DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 22 days ago by • 0 • written 11 months ago by • 0
1
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4
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343
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
16 days ago • updated 14 days ago winwater0928 • 0
1
vote
1
reply
137
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Handling multiple differential expression comparisons
DESeq2
updated 4 days ago by 42k • written 6 days ago by ▴ 10
1
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3
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234
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 13 days ago by 42k • written 14 days ago by • 0
1
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2
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246
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How to retrieve detailed regression results from deseq2
DESeq2
29 days ago • updated 20 days ago Weiqian ▴ 10
1
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2
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200
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Design Matrix within group comparison more than two groups
DESeq2
27 days ago • updated 26 days ago hemantcnaik • 0
1
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1
reply
131
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 9 days ago by 42k • written 9 days ago by • 0
1
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2
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721
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
22 days ago • updated 13 days ago ussarizona ▴ 10
1
vote
3
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257
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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 2 days ago by ★ 4.1k • written 8 days ago by • 0
1
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4
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491
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DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 8 days ago JKim • 0
1
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3
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221
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Different Shrunk Log2FC according with reference
DESeq2
updated 15 days ago by 42k • written 16 days ago by ▴ 20
0
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1
reply
121
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putting my own expression data in deseq2
DESeq2
updated 9 days ago by ★ 4.1k • written 9 days ago by • 0
0
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3
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266
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 8 days ago by 42k • written 9 days ago by • 0
0
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2
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163
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Deseq2 and Normalization of RNA sequencing data
DESeq2
8 days ago • updated 7 days ago kcarey • 0
0
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3
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168
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 7 days ago by ★ 4.1k • written 8 days ago by • 0
0
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1
reply
43
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normalization using Deseq2
DESeq2 rnaseqGene Normalization
updated 23 hours ago by ★ 4.1k • written 1 day ago by • 0
0
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1
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156
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 15 days ago by 42k • written 15 days ago by • 0
0
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1
reply
135
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Deseq2 Rlog transformation
DESeq2
updated 24 days ago by ★ 4.1k • written 26 days ago by • 0
0
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4
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277
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DEG with low counts
DESeq2
updated 20 days ago by 42k • written 25 days ago by • 0
0
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2
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125
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DESeq2 v1.35.0
DESeq2
updated 7 days ago by 42k • written 7 days ago by • 0
0
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7
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432
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DESeq filtering specific to contrasts
DESeq2
updated 20 days ago by 42k • written 12 weeks ago by • 0
0
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6
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242
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 6 days ago by ★ 1.4k • written 7 days ago by ▴ 130
0
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1
reply
135
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covariate with negative and positive values
DESeq2
updated 21 days ago by 42k • written 23 days ago by • 0
0
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1
reply
180
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DESeq2 gives an error and R crashes
DESeq2
29 days ago • updated 28 days ago Shefali • 0
0
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1
reply
153
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 21 days ago by ★ 4.1k • written 22 days ago by • 0
0
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4
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246
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
22 days ago • updated 20 days ago lonn • 0
0
votes
1
reply
115
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 21 days ago by 42k • written 21 days ago by • 0
0
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1
reply
142
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rlog transformation
DESeq2
updated 21 days ago by 42k • written 21 days ago by • 0
0
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1
reply
10
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 42 minutes ago by ★ 4.1k • written 48 minutes ago by • 0
0
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4
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608
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 23 days ago by 42k • written 6 months ago by • 0
0
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8
replies
361
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 15 days ago by ★ 1.4k • written 16 days ago by • 0
0
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2
replies
215
views
PCA plot suggestions
DESeq2 PCAtools
updated 13 days ago by 42k • written 15 days ago by • 0
0
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1
reply
137
views
Bioinformatics student
Des DESeq2
updated 27 days ago by • 0 • written 27 days ago by • 0
0
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3
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209
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 23 days ago by 42k • written 24 days ago by ▴ 20
0
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1
reply
120
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 9 days ago by 42k • written 10 days ago by • 0
0
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2
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142
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
10 days ago • updated 6 days ago Aurora • 0
45 results • Page 1 of 1
Recent ...
Replies
Answer: Differential gene expression analysis results by ATpoint ★ 4.1k
Pease do not open multiple posts for the same issue: https://support.bioconductor.org/p/9158194/#9158222 The support site is not meant f…
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results by swbarnes2 ★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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