Showing : StatisticalMethod • reset
2
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7
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1.4k
views
EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on individual patients not combined
edgeR StatisticalMethod
2.6 years ago Field -Ye • 0
6
votes
6
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1.7k
views
limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 10
6
votes
4
replies
974
views
Limma prametrization
limm MathematicalBiology limmaGUI StatisticalMethod
2.3 years ago Giovanni • 0
2
votes
4
replies
730
views
Model comparison in mean-dispersion trend in DESeq2
DESeq2 StatisticalMethod
14 months ago Loïc • 0
2
votes
3
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1.8k
views
deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 13 months ago by ★ 4.0k • written 13 months ago by • 0
1
vote
3
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1.1k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 3.2 years ago by 41k • written 3.2 years ago by • 0
2
votes
3
replies
3.1k
views
Differential gene expression and (adjusted) p-values
edgeR StatisticalMethod
updated 24 months ago by • 0 • written 2.2 years ago by • 0
1
vote
3
replies
885
views
Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 14 months ago by 50k • written 15 months ago by • 0
4
votes
2
replies
595
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 5 months ago by 50k • written 6 months ago by ▴ 10
0
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2
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1.3k
views
To retrieve the transcript from gff file with the longest isoform
FunctionalAnnotation StatisticalMethod
2.8 years ago Aneesha • 0
1
vote
2
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954
views
Limma adj.p.value the same for many different p.values
limmaGUI limma adj.p.value StatisticalMethod
19 months ago walkerrh95 • 0
2
votes
2
replies
593
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
3 months ago Linton • 0
0
votes
2
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721
views
Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?
PrincipalComponent StatisticalMethod edgeR MultidimensionalScaling Normalization
14 months ago rcreswell01 • 0
1
vote
2
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434
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
2
votes
2
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390
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
5 months ago Manthos • 0
3
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2
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663
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 10 months ago by 50k • written 10 months ago by ▴ 10
0
votes
2
replies
717
views
p adjusted value not available
StatisticalMethod DESeq2
updated 3.4 years ago by ★ 3.9k • written 3.4 years ago by • 0
0
votes
1
reply
525
views
DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 17 months ago by 41k • written 18 months ago by ▴ 10
0
votes
1
reply
730
views
DESeq2 Design matrix
StatisticalMethod DESeq2
updated 2.9 years ago by 41k • written 2.9 years ago by • 0
0
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0
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607
views
Job: Academic position in Non-clinical Biostatistics
JobPosting StatisticalMethod
17 months ago Laurent Gatto 1.6k
0
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0
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559
views
Should I adjust p value for multi-levels (groups) and multi-variables?
StatisticalMethod
2.1 years ago dong ▴ 10
0
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0
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1.2k
views
Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
3.3 years ago jol.espinoz ▴ 40
0
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0
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871
views
Job: Postdoctoral research scientist in computational biology/statistical genetics/functional genomics at Columbia University, USA
Alzheimer's StatisticalMethod Genetics molecularQTL FunctionalGenomics
19 months ago gaow • 0
23 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Votes
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
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