Showing : deseq2 • reset
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votes
6
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150
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 6 hours ago by ★ 1.3k • written 1 day ago by ▴ 130
2
votes
2
replies
98
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 17 hours ago by 41k • written 17 hours ago by • 0
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0
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31
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Handling multiple differential expression comparisons
DESeq2
18 hours ago Zainab • 0
0
votes
2
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107
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Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
4 days ago • updated 1 day ago Aurora • 0
0
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2
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107
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Deseq2 and Normalization of RNA sequencing data
DESeq2
2 days ago • updated 1 day ago kcarey • 0
0
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2
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73
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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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110
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
0
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3
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231
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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
votes
1
reply
118
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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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473
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DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 2 days ago JKim • 0
6
votes
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 3 days ago by • 0 • written 4.6 years ago by ▴ 10
1
vote
1
reply
93
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 3 days ago by 41k • written 4 days ago by • 0
0
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1
reply
92
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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
votes
1
reply
93
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putting my own expression data in deseq2
DESeq2
updated 4 days ago by ★ 4.1k • written 4 days ago by • 0
3
votes
3
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206
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DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 5 days ago by ★ 4.1k • written 5 days ago by ▴ 10
0
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2
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191
views
PCA plot suggestions
DESeq2 PCAtools
updated 7 days ago by 41k • written 9 days ago by • 0
1
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2
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700
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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
vote
3
replies
199
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 7 days ago by 41k • written 8 days ago by • 0
1
vote
4
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312
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
10 days ago • updated 8 days ago winwater0928 • 0
2
votes
9
replies
357
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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 9 days ago by • 0
0
votes
8
replies
337
views
DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 9 days ago by ★ 1.3k • written 10 days ago by • 0
0
votes
1
reply
142
views
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
vote
3
replies
205
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Different Shrunk Log2FC according with reference
DESeq2
updated 10 days ago by 41k • written 10 days ago by ▴ 20
3
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1
reply
302
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 10 days ago by 41k • written 10 days ago by ▴ 40
3
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3
replies
220
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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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234
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
16 days ago • updated 14 days ago lonn • 0
1
vote
2
replies
239
views
How to retrieve detailed regression results from deseq2
DESeq2
23 days ago • updated 14 days ago Weiqian ▴ 10
0
votes
7
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413
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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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744
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DESeq2 setting significant p-value
DESeq2
updated 14 days ago by 41k • written 5.0 years ago by ▴ 10
0
votes
4
replies
261
views
DEG with low counts
DESeq2
updated 15 days ago by 41k • written 19 days ago by • 0
0
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1
reply
132
views
rlog transformation
DESeq2
updated 15 days ago by 41k • written 16 days ago by • 0
0
votes
1
reply
109
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ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 15 days ago by 41k • written 16 days ago by • 0
0
votes
1
reply
130
views
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
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 15 days ago by • 0 • written 8.8 years ago by ▴ 30
0
votes
1
reply
142
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 16 days ago by ★ 4.1k • written 16 days ago by • 0
2
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5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 17 days ago by • 0 • written 10 months ago by • 0
0
votes
4
replies
595
views
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
votes
3
replies
203
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 17 days ago by 41k • written 18 days ago by ▴ 20
0
votes
1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 19 days ago by ★ 4.1k • written 20 days ago by • 0
1
vote
2
replies
191
views
Design Matrix within group comparison more than two groups
DESeq2
21 days ago hemantcnaik • 0
0
votes
1
reply
131
views
Bioinformatics student
Des DESeq2
updated 21 days ago by • 0 • written 21 days ago by • 0
0
votes
1
reply
174
views
DESeq2 gives an error and R crashes
DESeq2
23 days ago • updated 22 days ago Shefali • 0
0
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2
replies
218
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 24 days ago by 41k • written 29 days ago by ▴ 30
0
votes
1
reply
160
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 24 days ago by 41k • written 24 days ago by • 0
0
votes
2
replies
239
views
Regressing out batch effects
DESeq2
updated 24 days ago by 41k • written 29 days ago by • 0
0
votes
2
replies
165
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
vote
1
reply
164
views
DESeq2 - Missing values in count matrix
DESeq2
updated 29 days ago by 65k • written 29 days ago by • 0
1
vote
6
replies
430
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
0
votes
2
replies
171
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
4 weeks ago michelafrancesconi8 • 0
1
vote
1
reply
152
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago Layal • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
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!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
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
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