Showing : StatisticalMethod • reset
2
votes
2
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551
views
DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
3 months ago Linton • 0
1
vote
2
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420
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago • updated 3 months ago Sabiha ▴ 20
2
votes
2
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384
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 • updated 4 months ago Manthos • 0
4
votes
2
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571
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 5 months ago by 50k • written 5 months ago by ▴ 10
3
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2
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657
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
2
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3
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1.7k
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deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 12 months ago by ★ 4.0k • written 13 months ago by • 0
2
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4
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724
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Model comparison in mean-dispersion trend in DESeq2
DESeq2 StatisticalMethod
14 months ago Loïc • 0
0
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2
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714
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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
3
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876
views
Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 14 months ago by 50k • written 14 months ago by • 0
0
votes
1
reply
520
views
DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 16 months ago by 41k • written 17 months ago by ▴ 10
0
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0
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592
views
Job: Academic position in Non-clinical Biostatistics
JobPosting StatisticalMethod
17 months ago Laurent Gatto 1.6k
1
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2
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939
views
Limma adj.p.value the same for many different p.values
limmaGUI limma adj.p.value StatisticalMethod
18 months ago walkerrh95 • 0
0
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0
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859
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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
2
votes
3
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3.1k
views
Differential gene expression and (adjusted) p-values
edgeR StatisticalMethod
updated 23 months ago by • 0 • written 2.2 years ago by • 0
0
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0
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555
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Should I adjust p value for multi-levels (groups) and multi-variables?
StatisticalMethod
2.1 years ago dong ▴ 10
6
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4
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967
views
Limma prametrization
limm MathematicalBiology limmaGUI StatisticalMethod
2.3 years ago • updated 2.2 years ago Giovanni • 0
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
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
0
votes
1
reply
725
views
DESeq2 Design matrix
StatisticalMethod DESeq2
updated 2.9 years ago by 41k • written 2.9 years ago by • 0
6
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6
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1.6k
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
1
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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
0
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0
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1.2k
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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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2
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714
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p adjusted value not available
StatisticalMethod DESeq2
updated 3.4 years ago by ★ 3.9k • written 3.4 years ago by • 0
23 results • Page 1 of 1
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Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You that there are "too many low-reads" but actually there …
Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Answer: Finding DEGs by using edgeR by Gordon Smyth 50k
I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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