Showing : RNASEQ • reset
3
votes
5
replies
193
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Getting batch corrected counts after RUVSeq
BatchEffect RUVSeq RNASeq DESeq2
updated 11 days ago by ★ 3.4k • written 12 days ago by • 0
1
vote
1
reply
116
views
bulk RNA-Seq batch correction
RNASeqData rnaseqcomp RNASeq
updated 16 days ago by ★ 3.4k • written 17 days ago by • 0
0
votes
1
reply
240
views
DESeq design and contrast with multiple factors
RNASeq DESeq2
updated 17 days ago by 40k • written 23 days ago by • 0
1
vote
6
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360
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Time-series RNA-seq analysis using DESeq2
time-series DESeq2 RNASeq timecoursedata TimeCourse
updated 5 weeks ago by ★ 3.4k • written 5 weeks ago by • 0
5
votes
7
replies
311
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Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 7 weeks ago by 48k • written 7 weeks ago by • 0
0
votes
1
reply
298
views
Is it proper to compare two WGCNA matrixes if they were raised to different power (soft threshold)?
Network cluster WGCNA RNASeq
updated 8 weeks ago by 63k • written 8 weeks ago by • 0
2
votes
1
reply
250
views
Grouping DEGs yields varying results
RNASeq limma
updated 8 weeks ago by 48k • written 8 weeks ago by • 0
2
votes
5
replies
473
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Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 weeks ago • updated 8 weeks ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
249
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Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
9 weeks ago Matteo • 0
3
votes
2
replies
376
views
Gene set analysis: GSVA, Z-Score, and fold-changes
GSVA RNASeq limma
updated 11 weeks ago by 48k • written 11 weeks ago by • 0
0
votes
3
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286
views
Multiple Testing When Using Multiple Contrasts/Comparisons in DESEQ2
MultipleComparison DESeq2 Genetics contrasts RNASeq
updated 10 weeks ago by 63k • written 11 weeks ago by • 0
0
votes
1
reply
332
views
Genes with highest differential expression have very low read counts for most genes
RNASeq depmap DESeq2
updated 3 months ago by 40k • written 4 months ago by • 0
3
votes
11
replies
981
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Adjusting for baseline when having longitudinal data, mixed model and no treatment
RNAseq mixedmodels baselineadjustement limma
4 months ago • updated 3 months ago Anna ▴ 20
1
vote
9
replies
4.4k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 5.6 years ago by • 0
0
votes
1
reply
283
views
CI for logCPM (fitted values)
RNAseq edgeR
updated 4 months ago by 48k • written 4 months ago by ▴ 10
3
votes
4
replies
407
views
Anova table edgeR limma
limma RNASeq edgeR
4 months ago KATHERINE CHUERE NUNES • 0
1
vote
2
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285
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 4 months ago by 48k • written 4 months ago by • 0
0
votes
3
replies
418
views
Account for heteroscedasticity when fitting gene expression data
RNAseq
updated 4 months ago by 40k • written 4 months ago by • 0
0
votes
2
replies
409
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 4 months ago by • 0
1
vote
3
replies
421
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 4 months ago by 48k • written 4 months ago by • 0
0
votes
2
replies
431
views
model matrix not full rank
DESeq2 RNASeq
updated 4 months ago by • 0 • written 4 months ago by • 0
0
votes
1
reply
249
views
What is the correct way to split genex_high and genex_low groups for DE analysis?
DESeq2 RNASeq
updated 4 months ago by 40k • written 5 months ago by • 0
2
votes
3
replies
291
views
RNA seq with edgeR with several factors
RNAseq factors
5 months ago • updated 4 months ago Nathalie ▴ 20
0
votes
3
replies
445
views
edgeR DEGs multilevel
edgeR RNASeq DifferentialRegulation
updated 4 months ago by 48k • written 5 months ago by • 0
7
votes
8
replies
9.3k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 5 months ago by ★ 3.4k • written 7.1 years ago by ▴ 20
0
votes
4
replies
385
views
Combine RNA-seq
BatchEffect R rnaseq
updated 5 months ago by ★ 1.3k • written 5 months ago by • 0
1
vote
1
reply
298
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2 edgeR RNAseq
updated 5 months ago by 48k • written 5 months ago by • 0
3
votes
12
replies
771
views
Unwanted variation observed on PCA for transcript level data
salmon RUVSeq cqn PCA RNASeq
updated 5 months ago by 40k • written 5 months ago by ▴ 10
0
votes
1
reply
248
views
Sample expression calculation in rna seq
Rnaseq
updated 5 months ago by ★ 3.4k • written 5 months ago by • 0
1
vote
1
reply
267
views
Can I run deseq2 on two separate experiments at once?
rnaseq deseq2
updated 5 months ago by ★ 3.4k • written 5 months ago by • 0
0
votes
0
replies
296
views
WGCNA approach on multiregional brain transcriptomes
Neurotranscriptome RNAseq WGCNA
5 months ago Levi • 0
4
votes
8
replies
2.5k
views
Interpreting ellipses in PCAtools for bulk RNAseq
ellipse RNAseq PCAtools
updated 5 months ago by • 0 • written 2.3 years ago by • 0
1
vote
2
replies
312
views
RNA-Seq normalization of pre and post treatment groups
Normalization RNASeq
written 5 months ago by • 0
2
votes
4
replies
456
views
limma with or without intercept gives different results
limma rnaseq
6 months ago • updated 5 months ago Sydney • 0
1
vote
2
replies
524
views
RUVSeq and DESeq2 -- all variables in design formula must be columns in colData
DESeq2 RNAseq RUVSeq
6 months ago garbuzov • 0
0
votes
2
replies
295
views
Compare and filter three BAM files
RNAseq 10X
6 months ago wt215 • 0
0
votes
5
replies
490
views
hill-shaped p-value distributions using EdgeR
edgeR p-valuedistribution RNAseq hill-shaped
updated 6 months ago by 48k • written 6 months ago by • 0
5
votes
6
replies
612
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 6 months ago by ▴ 40 • written 6 months ago by • 0
0
votes
2
replies
378
views
GO analysis in R vs website
GO RNASeq
6 months ago Nitro • 0
1
vote
4
replies
424
views
Repeated Measures-Cross Over Study for RNAseq data using variancePartition::dream
RNAseq variancePartition edgeR dream
6 months ago DH • 0
1
vote
0
replies
387
views
Job: Seeking collaborator/contractor (paid) for Bioconductor package development
RNASeq JobPosting
6 months ago Jamie Walters ▴ 10
3
votes
2
replies
358
views
Batch question Bulk RNA-Seq
BatchEffect RNASeq
6 months ago chf • 0
0
votes
1
reply
320
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 6 months ago by ★ 3.4k • written 6 months ago by • 0
1
vote
1
reply
290
views
Subsetting DESeq when different cell types
DESeq2 RNASeq
updated 6 months ago by ★ 3.4k • written 6 months ago by ▴ 20
0
votes
7
replies
803
views
Weird dispersion and volcano plots in DEA with paired samples
DESeq2 RNASeq
updated 6 months ago by 40k • written 6 months ago by • 0
0
votes
2
replies
469
views
PCA subset of genes vs DE
DESeq2 RNASeq
6 months ago andrebolerbarros ▴ 20
2
votes
5
replies
656
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 6 months ago by • 0
0
votes
3
replies
449
views
Understanding edgeR differential expression results
Transcriptomics edgeR DifferentialExpression RNASeqData RNASeq
updated 7 months ago by 48k • written 7 months ago by • 0
0
votes
2
replies
419
views
combining multiple salmon runs after tximport
tximport RNASeq salmon
updated 7 months ago by ★ 3.4k • written 7 months ago by • 0
0
votes
1
reply
434
views
Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
updated 7 months ago by ★ 3.4k • written 7 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
Thank you, I have a very clear understanding of the situation. > COO_Sparse_HDF5RealizationSink(), writeHDF5SparseArray(), COO_H5SparseArr…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
There are a few places inside my `DelayedTensor` package that use `SparseArraySeed`. Will these stop working in next coming BioC 3.18, whe…
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
No. But I will need to modify the `write_block()` method for TENxRealizationSink implemented in **HDF5Array** to make it handle blocks that…
Answer: ''Model_Matrix'' error by Gordon Smyth 48k
This is actually an error message from base R rather than from limma. The error says that `Group` contains 0 or 1 levels, so your assumptio…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
> I don't know the details but do you mean using HDF5RealizationSink or TENxRealizationSink will make it possible to writing sparse multi-d…
Votes
Steps needed to change design (relevel factors) in DESeq2
Steps needed to change design (relevel factors) in DESeq2
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
Awards • All
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