Showing : DEseq2 • reset
2
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10
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4.6k
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DESeq2 results export padj sorted
deseq2 deseq differential binding analysis
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 60
2
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4
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2.8k
views
Matrix not full rank - DESeq2
deseq2 model matrix not full rank model.matrix deseq differential binding analysis
updated 7.9 years ago by ★ 3.8k • written 7.9 years ago by ▴ 60
2
votes
2
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2.3k
views
RNAseq analysis: how to compare two very different samples?
edgeR deseq2 RNAseq
updated 7.9 years ago by ★ 29k • written 7.9 years ago by ▴ 10
3
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2
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7.0k
views
Remove one sample from DESeq2 subject
deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 20
1
vote
3
replies
869
views
Is it reasonable to use rlog difference to reflect differential expression of a gene across samples, and rlog value to reflect the expression level
deseq2 rnaseq
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
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2
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2.2k
views
DESeq2 - Design for TCGA unpaired RNAseq data
DESeq2 design TCGA unpaired RNAseq
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 10
3
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4
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2.4k
views
Use interactions to get the difference in the effect of two treatments
deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 70
1
vote
1
reply
806
views
What do you do with the DESeq2 NA results ?. How do you manage them ?
DESeq2 NA values
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 130
9
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1
reply
5.5k
views
Should I contrast 2 treatment groups using the control group as reference or directly against each other?
deseq2 model.matrix GLM contrast
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 60
3
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2
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1.4k
views
DESeq2 1.16.1 : Zero count values re-occurrence of issue 56191?
deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
1
vote
12
replies
4.8k
views
DESeq2 LFC shrinkage is for designs with interactions
deseq2 lfcshrink
7.9 years ago yk.gatc • 0
0
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5
replies
1.2k
views
results function of DESeq2 devel fails
deseq2
7.9 years ago unamourdeswann ▴ 10
0
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1
reply
1.0k
views
result from DESeq2 is hard to explain
deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
0
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3
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1.4k
views
DESeq2: would 'contrast' work for serial experiments?
DESeq2 mirna-seq small RNA-seq
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 40
0
votes
1
reply
826
views
Difference between unifactorial and two-factorial analysis
deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
4
votes
14
replies
8.6k
views
DESeq2: Question about the alpha in summary() and results()
deseq2
updated 2.9 years ago by ▴ 10 • written 7.9 years ago by ▴ 270
11
votes
14
replies
14k
views
Is there a conceptual difference between vst/rlog transforms and lfcShrink?
deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 40
0
votes
5
replies
1.1k
views
Are interaction terms symetrical with regard to the designation of main and secondary effect?
deseq2
7.9 years ago kieran.mace ▴ 40
9
votes
2
replies
6.9k
views
log fold change threshold in Deseq2 - using lfcthreshold
lfcthreshold deseq2
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 80
0
votes
1
reply
1.6k
views
Base mean count threshold
deseq2 base
updated 7.9 years ago by 43k • written 7.9 years ago by ▴ 80
1
vote
2
replies
1.7k
views
Differential expression of RNA seq data at gene level (for Beginner)
deseq2 differential gene expression bioconductor
updated 7.9 years ago by ▴ 130 • written 7.9 years ago by • 0
0
votes
1
reply
939
views
Multiple tests in a single deseq object
deseq2
updated 7.9 years ago by ★ 13k • written 7.9 years ago by ▴ 40
2
votes
3
replies
2.0k
views
Can DESeq2/edgeR perform differential analysis for rRNA?
deseq2 edger rRNA differential gene expression
7.9 years ago r.aprianto ▴ 30
2
votes
2
replies
2.8k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger deseq2
updated 2.3 years ago by • 0 • written 8.0 years ago by • 0
1
vote
2
replies
729
views
coef funcition execept for pvalues
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 40
0
votes
10
replies
20k
views
Differential expression due to extreme outliers in DESeq2
deseq2 outliers
8.0 years ago paul.alto ▴ 50
2
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2
replies
3.4k
views
fdrtool - How does it work?
fdrtool deseq2
8.0 years ago rrcutler ▴ 70
1
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2
replies
1.3k
views
RNAseq tximport Deseq2
deseq2 tximport
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 30
2
votes
5
replies
1.8k
views
Mapping DESeq2 output back to chromosomal positions
deseq2 deseq diffbind differential binding analysis
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
1
vote
3
replies
1.4k
views
Supplying a designmatrix to DESeq()
deseq2
8.0 years ago kieran.mace ▴ 40
3
votes
4
replies
4.0k
views
TWO-way analysis with DESeq2 - obtaining p-values for the fixed factors and the interaction
DESeq2 Two-way analysis deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 40
1
vote
3
replies
4.0k
views
Batch effect removal with Deseq2
deseq2 batch effect removebatcheffect() limma
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 80
1
vote
3
replies
804
views
Multiple comparisons in DESeq2
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 10
0
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3
replies
1.8k
views
Deseq2: 3 factors design
deseq2 multiple factor design
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
0
votes
1
reply
903
views
DESeq2 design matrix
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 10
1
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1
reply
1.4k
views
DESeq2 contrasts within group only comparing against one level
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
1
vote
3
replies
1.3k
views
Testing moderated fold changes in DESeq2 version >= 1.16.0
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 30
2
votes
4
replies
1.6k
views
How to judge DESeq2_block and EdgeR_block result
diffbind Deseq2 edger differential binding analysis
updated 8.0 years ago by ★ 5.2k • written 8.0 years ago by • 0
1
vote
5
replies
8.4k
views
DESeq2 and edgeR getting very different results
edger deseq2 differential expression
updated 8.0 years ago by ▴ 20 • written 8.0 years ago by • 0
4
votes
3
replies
1.7k
views
Opinions on DESeqDataSetFromMatrix rowSums minimum for ChIP and/or ATAC-seq
deseq2 atac-seq chipseq differential binding analysis
updated 8.0 years ago by ★ 29k • written 8.0 years ago by ▴ 60
0
votes
4
replies
1.5k
views
Missing condition information from colData in DESeq2 gives enormous False Positives?
deseq2
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 20
0
votes
3
replies
1.8k
views
disagreement between log2FoldChange and lfcMLE in DESeq2
deseq2 log2fc shrinkage
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 90
1
vote
2
replies
1.4k
views
DESeq possible when only rlog table available? (DESeq2 package)
deseq2 rlog deseq
8.0 years ago sreibe • 0
1
vote
5
replies
5.6k
views
DESeq2 model design using continuous viable only
deseq2 mikelove
updated 4.4 years ago by 43k • written 8.0 years ago by • 0
0
votes
6
replies
2.0k
views
contamination and DESeq2 performance
deseq2 low count genes independent filtering
updated 8.0 years ago by ▴ 20 • written 8.0 years ago by ▴ 20
0
votes
2
replies
1.4k
views
Single and double mutant DEG analysis using DESeq2
deseq2 batch effect rnaseq
updated 8.0 years ago by 43k • written 8.0 years ago by • 0
9
votes
17
replies
2.6k
views
DESeq2 design subcategories
deseq2 deseq differential binding analysis
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 60
0
votes
4
replies
1.2k
views
DESeq2 76% of genes labeled 'low count'
deseq2 low count genes
updated 8.0 years ago by 43k • written 8.0 years ago by ▴ 20
2
votes
6
replies
3.0k
views
DESeq: Question about contrast and group-wise subsetting.
deseq2 deseq
8.0 years ago Bioinformatician_R ▴ 20
2
votes
4
replies
2.1k
views
Multiple test corrections for planed contrasts
deseq2 multiple comparisons contrast
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 60
4,840 results • Page 68 of 97
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Comment: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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