Showing : DeSeq2 • reset
9
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12
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7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 14 days ago by • 0 • written 8.8 years ago by ▴ 30
6
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19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by • 0 • written 4.6 years ago by ▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect RNASeqData WGCNA DESeq2
updated 15 days ago by • 0 • written 10 months ago by • 0
2
votes
5
replies
735
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DESeq2 setting significant p-value
DESeq2
updated 13 days ago by 41k • written 5.0 years ago by ▴ 10
1
vote
2
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694
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
15 days ago • updated 6 days ago ussarizona ▴ 10
0
votes
4
replies
592
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 16 days ago by 41k • written 6 months ago by • 0
1
vote
4
replies
456
views
DEseq2 coefficient
DESeq2 coefficient
9 weeks ago • updated 1 day ago JKim • 0
1
vote
6
replies
419
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DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2 Normalization
updated 28 days ago by 41k • written 29 days ago by • 0
0
votes
7
replies
405
views
DESeq filtering specific to contrasts
DESeq2
updated 13 days ago by 41k • written 11 weeks ago by • 0
2
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9
replies
342
views
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 7 days ago by • 0
0
votes
8
replies
323
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DESeq2 output used for PCA plot on R studio
DESeq2 RSTUDIO PCAtools
updated 7 days ago by ★ 1.3k • written 9 days ago by • 0
1
vote
4
replies
301
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Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago winwater0928 • 0
3
votes
1
reply
297
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 8 days ago by 41k • written 9 days ago by ▴ 40
0
votes
4
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260
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DEG with low counts
DESeq2
updated 13 days ago by 41k • written 18 days ago by • 0
1
vote
2
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239
views
How to retrieve detailed regression results from deseq2
DESeq2
22 days ago • updated 13 days ago Weiqian ▴ 10
0
votes
2
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233
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Regressing out batch effects
DESeq2
updated 23 days ago by 41k • written 28 days ago by • 0
0
votes
4
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229
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Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind DESeq2 ATACSeq
15 days ago • updated 12 days ago lonn • 0
0
votes
3
replies
217
views
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
votes
2
replies
214
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 22 days ago by 41k • written 27 days ago by ▴ 30
3
votes
3
replies
213
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DESeq2 - dispersion estimation when there is none
DESeq2
updated 9 days ago by 41k • written 10 days ago by • 0
1
vote
3
replies
202
views
Different Shrunk Log2FC according with reference
DESeq2
updated 8 days ago by 41k • written 8 days ago by ▴ 20
0
votes
3
replies
200
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 16 days ago by 41k • written 17 days ago by ▴ 20
3
votes
3
replies
197
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2 contrasts
updated 3 days ago by ★ 4.1k • written 3 days ago by ▴ 10
1
vote
2
replies
189
views
Design Matrix within group comparison more than two groups
DESeq2
20 days ago • updated 19 days ago hemantcnaik • 0
1
vote
3
replies
187
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2 celda
updated 6 days ago by 41k • written 7 days ago by • 0
0
votes
2
replies
182
views
PCA plot suggestions
DESeq2 PCAtools
updated 6 days ago by 41k • written 7 days ago by • 0
0
votes
1
reply
173
views
DESeq2 gives an error and R crashes
DESeq2
22 days ago • updated 21 days ago Shefali • 0
0
votes
2
replies
167
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2 sva
4 weeks ago • updated 29 days ago michelafrancesconi8 • 0
0
votes
2
replies
161
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 27 days ago by 65k • written 27 days ago by • 0
1
vote
1
reply
160
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DESeq2 - Missing values in count matrix
DESeq2
updated 28 days ago by 65k • written 28 days ago by • 0
0
votes
1
reply
157
views
IgG control in RIP-seq with Deseq2
DESeq2 RIP-seq
updated 23 days ago by 41k • written 23 days ago by • 0
1
vote
1
reply
150
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago • updated 29 days ago Layal • 0
0
votes
1
reply
139
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 14 days ago by ★ 4.1k • written 15 days ago by • 0
0
votes
1
reply
131
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 8 days ago by 41k • written 8 days ago by • 0
0
votes
1
reply
130
views
Bioinformatics student
Des DESeq2
updated 20 days ago by • 0 • written 20 days ago by • 0
0
votes
1
reply
128
views
Deseq2 Rlog transformation
DESeq2
updated 17 days ago by ★ 4.1k • written 18 days ago by • 0
0
votes
1
reply
128
views
covariate with negative and positive values
DESeq2
updated 14 days ago by 41k • written 16 days ago by • 0
0
votes
1
reply
123
views
rlog transformation
DESeq2
updated 14 days ago by 41k • written 14 days ago by • 0
0
votes
1
reply
106
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 14 days ago by 41k • written 14 days ago by • 0
0
votes
1
reply
98
views
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
0
votes
3
replies
93
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 13 hours ago by ★ 4.1k • written 1 day ago by • 0
0
votes
1
reply
86
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by 41k • written 3 days ago by • 0
0
votes
1
reply
85
views
putting my own expression data in deseq2
DESeq2
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
1
vote
1
reply
81
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind ChIPSeqData DESeq2
updated 2 days ago by 41k • written 2 days ago by • 0
0
votes
1
reply
75
views
Timecourse RNASeq analysis
DESeq2 ImpulseDE2 timecour timecoursedata moanin
updated 2 days ago by 41k • written 2 days ago by • 0
0
votes
2
replies
59
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
1 day ago • updated 1 hour ago kcarey • 0
0
votes
3
replies
49
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
3 hours ago arfranco ▴ 130
0
votes
2
replies
48
views
DESeq2 v1.35.0
DESeq2
updated 7 hours ago by 41k • written 8 hours ago by • 0
48 results • Page 1 of 1
Recent ...
Replies
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 …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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