Showing : deseq2 • reset
2
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66
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 3 hours ago by 41k • written 3 hours ago by • 0
0
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0
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17
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Handling multiple differential expression comparisons
DESeq2
4 hours ago Zainab • 0
0
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5
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121
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 9 hours ago by 65k • written 1 day ago by ▴ 130
0
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2
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103
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
3 days ago • updated 13 hours ago Aurora • 0
0
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2
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100
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Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 23 hours ago kcarey • 0
0
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2
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66
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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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107
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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
0
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3
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226
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
0
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1
reply
109
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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 2 days 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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88
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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
reply
90
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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 4 days ago by • 0
0
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1
reply
90
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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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201
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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
0
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2
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189
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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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699
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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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195
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 7 days ago by 41k • written 8 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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354
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 8 days ago by 65k • written 8 days ago by • 0
0
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8
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333
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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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139
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DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 9 days ago by 41k • written 9 days ago by • 0
1
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3
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205
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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
reply
302
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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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218
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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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233
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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
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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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261
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DEG with low counts
DESeq2
updated 14 days ago by 41k • written 19 days ago by • 0
0
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1
reply
131
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rlog transformation
DESeq2
updated 15 days ago by 41k • written 15 days ago by • 0
0
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1
reply
108
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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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130
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covariate with negative and positive values
DESeq2
updated 15 days ago by 41k • written 17 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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141
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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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595
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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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202
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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
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129
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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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191
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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 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
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2
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163
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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
vote
1
reply
163
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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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427
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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
48 results • Page 1 of 1
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Replies
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
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…
Votes
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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