Showing : deseq2 • reset
2
votes
2
replies
90
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 9 hours ago by 41k • written 10 hours ago by • 0
0
votes
0
replies
24
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Handling multiple differential expression comparisons
DESeq2
10 hours ago Zainab • 0
0
votes
5
replies
126
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 16 hours ago by 65k • written 1 day ago by ▴ 130
0
votes
2
replies
103
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
3 days ago • updated 19 hours ago Aurora • 0
0
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2
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104
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Deseq2 and Normalization of RNA sequencing data
DESeq2
2 days ago • updated 1 day ago kcarey • 0
0
votes
2
replies
71
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DESeq2 v1.35.0
DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
0
votes
3
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109
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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 2 days ago by • 0
0
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3
replies
229
views
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
114
views
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
vote
4
replies
472
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DEseq2 coefficient
DESeq2 coefficient
10 weeks ago • updated 2 days ago JKim • 0
6
votes
19
replies
2.5k
views
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
91
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 3 days ago by 41k • written 3 days ago by • 0
0
votes
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
votes
1
reply
92
views
putting my own expression data in deseq2
DESeq2
updated 3 days ago by ★ 4.1k • written 3 days ago by • 0
3
votes
3
replies
203
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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 5 days ago by ▴ 10
0
votes
2
replies
189
views
PCA plot suggestions
DESeq2 PCAtools
updated 7 days ago by 41k • written 9 days ago by • 0
1
vote
2
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699
views
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
197
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 7 days ago by 41k • written 8 days ago by • 0
1
vote
4
replies
309
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
9 days ago • updated 7 days ago winwater0928 • 0
2
votes
9
replies
355
views
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
votes
8
replies
334
views
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
votes
1
reply
140
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
views
Different Shrunk Log2FC according with reference
DESeq2
updated 9 days ago by 41k • written 9 days ago by ▴ 20
3
votes
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
votes
3
replies
219
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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
votes
4
replies
233
views
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
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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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
replies
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 14 days ago by 41k • written 19 days ago by • 0
0
votes
1
reply
132
views
rlog transformation
DESeq2
updated 15 days ago by 41k • written 15 days ago by • 0
0
votes
1
reply
109
views
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
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
votes
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
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
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 16 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
202
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 18 days ago by ★ 4.1k • written 19 days ago by • 0
1
vote
2
replies
191
views
Design Matrix within group comparison more than two groups
DESeq2
21 days ago • updated 20 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
votes
2
replies
215
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 24 days ago by 41k • written 28 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
238
views
Regressing out batch effects
DESeq2
updated 24 days ago by 41k • written 29 days ago by • 0
0
votes
2
replies
164
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
163
views
DESeq2 - Missing values in count matrix
DESeq2
updated 29 days ago by 65k • written 29 days ago by • 0
1
vote
6
replies
429
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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: 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!
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…
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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