Showing : DESeq2 • reset
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votes
6
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169
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Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 18 hours ago by ★ 1.3k • written 2 days ago by ▴ 130
2
votes
2
replies
111
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 1 day ago by 41k • written 1 day ago by • 0
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0
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39
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Handling multiple differential expression comparisons
DESeq2
1 day ago Zainab • 0
0
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2
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78
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DESeq2 v1.35.0
DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
0
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2
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113
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Deseq2 and Normalization of RNA sequencing data
DESeq2
3 days ago • updated 2 days ago kcarey • 0
0
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3
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114
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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 3 days ago by • 0
0
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1
reply
121
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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 3 days ago by ★ 4.1k • written 3 days ago by • 0
0
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3
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234
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log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 3 days ago by 41k • written 4 days ago by • 0
1
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1
reply
95
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Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 4 days ago by 41k • written 4 days ago by • 0
0
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2
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109
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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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1
reply
93
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Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 4 days ago by 41k • written 5 days ago by • 0
0
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1
reply
94
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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
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3
replies
212
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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
votes
2
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197
views
PCA plot suggestions
DESeq2 PCAtools
updated 8 days ago by 41k • written 9 days ago by • 0
1
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3
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206
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Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 8 days ago by 41k • written 9 days ago by • 0
2
votes
9
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371
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2 RUVSeq RUVseq BatchEffect DES
updated 9 days ago by 65k • written 9 days ago by • 0
0
votes
1
reply
146
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 10 days ago by 41k • written 10 days ago by • 0
1
vote
3
replies
206
views
Different Shrunk Log2FC according with reference
DESeq2
updated 10 days ago by 41k • written 10 days ago by ▴ 20
1
vote
4
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314
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
10 days ago • updated 8 days ago winwater0928 • 0
3
votes
1
reply
305
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 10 days ago by 41k • written 11 days ago by ▴ 40
0
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8
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340
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 9 days ago by ★ 1.3k • written 11 days ago by • 0
3
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3
replies
220
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 11 days ago by 41k • written 12 days ago by • 0
0
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1
reply
133
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rlog transformation
DESeq2
updated 16 days ago by 41k • written 16 days ago by • 0
0
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1
reply
111
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 16 days ago by 41k • written 16 days ago by • 0
1
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2
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705
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
17 days ago • updated 8 days ago ussarizona ▴ 10
0
votes
1
reply
130
views
covariate with negative and positive values
DESeq2
updated 16 days ago by 41k • written 18 days ago by • 0
0
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1
reply
146
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DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 16 days ago by ★ 4.1k • written 17 days ago by • 0
0
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4
replies
235
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
17 days ago • updated 14 days ago lonn • 0
0
votes
3
replies
203
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 18 days ago by 41k • written 19 days ago by ▴ 20
1
vote
2
replies
240
views
How to retrieve detailed regression results from deseq2
DESeq2
24 days ago • updated 15 days ago Weiqian ▴ 10
0
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4
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262
views
DEG with low counts
DESeq2
updated 15 days ago by 41k • written 20 days ago by • 0
0
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1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 19 days ago by ★ 4.1k • written 20 days ago by • 0
1
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2
replies
193
views
Design Matrix within group comparison more than two groups
DESeq2
22 days ago • updated 21 days ago hemantcnaik • 0
0
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1
reply
132
views
Bioinformatics student
Des DESeq2
updated 22 days ago by • 0 • written 22 days ago by • 0
0
votes
1
reply
174
views
DESeq2 gives an error and R crashes
DESeq2
24 days ago • updated 23 days ago Shefali • 0
0
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2
replies
218
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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
161
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 25 days ago by 41k • written 25 days ago by • 0
0
votes
2
replies
244
views
Regressing out batch effects
DESeq2
updated 25 days ago by 41k • written 4 weeks ago by • 0
0
votes
2
replies
166
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 29 days ago by 65k • written 29 days ago by • 0
1
vote
1
reply
167
views
DESeq2 - Missing values in count matrix
DESeq2
updated 4 weeks ago by 65k • written 4 weeks ago by • 0
1
vote
6
replies
432
views
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
1
vote
1
reply
153
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago Layal • 0
0
votes
2
replies
171
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pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
4 weeks ago michelafrancesconi8 • 0
0
votes
4
replies
259
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
0
votes
1
reply
160
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
2
votes
3
replies
347
views
PCA of different bacterial species
DESeq2
updated 5 weeks ago by 41k • written 5 weeks ago by ▴ 10
0
votes
1
reply
169
views
collapseReplicates dimension error
DESeq2 Dese
updated 5 weeks ago by 41k • written 6 weeks ago by • 0
3
votes
2
replies
214
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2 Transcriptomics
5 weeks ago Anita ▴ 10
1
vote
2
replies
233
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
6 weeks ago • updated 5 weeks ago Chanderkant Chaudhary • 0
0
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2
replies
227
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Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
6 weeks ago kcarey • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
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 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
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…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
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
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