Showing : Deseq2 • reset
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated just now by 41k • written 18 minutes ago by • 0
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0
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9
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Handling multiple differential expression comparisons
DESeq2
1 hour ago Zainab • 0
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5
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115
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 6 hours ago by 65k • written 22 hours ago by ▴ 130
0
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2
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102
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
3 days ago • updated 9 hours ago Aurora • 0
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2
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91
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Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 19 hours ago kcarey • 0
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2
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64
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DESeq2 v1.35.0
DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
0
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3
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102
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 1 day ago by ★ 4.1k • written 1 day ago by • 0
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3
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223
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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
0
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1
reply
106
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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
1
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4
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463
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DEseq2 coefficient
DESeq2 coefficient
9 weeks ago • updated 2 days ago JKim • 0
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 3 days ago by • 0 • written 4.6 years ago by ▴ 10
1
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1
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87
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 3 days ago by 41k • written 3 days ago by • 0
0
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1
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88
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 3 days ago by 41k • written 3 days ago by • 0
0
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1
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88
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putting my own expression data in deseq2
DESeq2
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
3
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3
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200
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 4 days ago by ★ 4.1k • written 4 days ago by ▴ 10
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2
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188
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PCA plot suggestions
DESeq2 PCAtools
updated 7 days ago by 41k • written 8 days ago by • 0
1
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2
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697
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DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
16 days ago • updated 7 days ago ussarizona ▴ 10
1
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3
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194
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 7 days ago by 41k • written 7 days ago by • 0
1
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4
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308
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
9 days ago • updated 7 days ago winwater0928 • 0
2
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9
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351
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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 8 days ago by • 0
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8
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330
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 8 days ago by ★ 1.3k • written 10 days ago by • 0
0
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1
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137
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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 9 days ago by • 0
1
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3
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204
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Different Shrunk Log2FC according with reference
DESeq2
updated 9 days ago by 41k • written 9 days ago by ▴ 20
3
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1
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300
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Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 9 days ago by 41k • written 10 days ago by ▴ 40
3
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3
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216
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 10 days ago by 41k • written 11 days ago by • 0
0
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4
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232
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
16 days ago • updated 13 days ago lonn • 0
1
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2
replies
239
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How to retrieve detailed regression results from deseq2
DESeq2
22 days ago • updated 14 days ago Weiqian ▴ 10
0
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7
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410
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DESeq filtering specific to contrasts
DESeq2
updated 14 days ago by 41k • written 11 weeks ago by • 0
2
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5
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742
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DESeq2 setting significant p-value
DESeq2
updated 14 days ago by 41k • written 5.0 years ago by ▴ 10
0
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4
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260
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DEG with low counts
DESeq2
updated 14 days ago by 41k • written 18 days ago by • 0
0
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1
reply
130
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rlog transformation
DESeq2
updated 15 days ago by 41k • written 15 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 15 days ago by 41k • written 15 days ago by • 0
0
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1
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129
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covariate with negative and positive values
DESeq2
updated 15 days ago by 41k • written 16 days ago by • 0
9
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12
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7.8k
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Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 15 days ago by • 0 • written 8.8 years ago by ▴ 30
0
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1
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140
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 15 days ago by ★ 4.1k • written 16 days ago by • 0
2
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5
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1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 16 days ago by • 0 • written 10 months ago by • 0
0
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4
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594
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How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 17 days ago by 41k • written 6 months ago by • 0
0
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3
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201
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Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 17 days ago by 41k • written 18 days ago by ▴ 20
0
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1
reply
128
views
Deseq2 Rlog transformation
DESeq2
updated 18 days ago by ★ 4.1k • written 19 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
21 days ago • updated 20 days ago hemantcnaik • 0
0
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1
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130
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Bioinformatics student
Des DESeq2
updated 21 days ago by • 0 • written 21 days ago by • 0
0
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1
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174
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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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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 28 days ago by ▴ 30
0
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1
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160
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IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 23 days ago by 41k • written 24 days ago by • 0
0
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2
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238
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Regressing out batch effects
DESeq2
updated 23 days ago by 41k • written 29 days ago by • 0
0
votes
2
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161
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 28 days ago by 65k • written 28 days ago by • 0
1
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1
reply
162
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DESeq2 - Missing values in count matrix
DESeq2
updated 29 days ago by 65k • written 29 days ago by • 0
1
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6
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420
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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 4 weeks ago by • 0
0
votes
2
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171
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
4 weeks ago michelafrancesconi8 • 0
1
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1
reply
150
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DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago Layal • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
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 …
Votes
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
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