Showing : StatisticalMethod • reset
3
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4
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545
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p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 3 months ago by • 0 • written 4 months ago by • 0
0
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248
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
8 months ago user_bioinfo • 0
1
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2
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471
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Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData signatureSearchData StatisticalMethod
written 13 months ago by • 0
0
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1
reply
736
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Can we compare 3 different experimental conditions with DESeq2?
DESeq2 StatisticalMethod
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
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0
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642
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Job: Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod Evolution QuantitativeTrailLocus Genetics JobPosting
19 months ago pierre.devillemereuil • 0
0
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3
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1.5k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
2
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2
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3.7k
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
23 months ago Linton • 0
1
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2
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1.3k
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
2.0 years ago • updated 24 months ago Sabiha ▴ 20
2
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2
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1.1k
views
DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
2.1 years ago Manthos • 0
5
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2
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2.2k
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DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 2.1 years ago by 53k • written 2.1 years ago by ▴ 10
3
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2
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1.2k
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Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 30
2
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3
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3.7k
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deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
2
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4
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1.2k
views
Model comparison in mean-dispersion trend in DESeq2
DESeq2 StatisticalMethod
2.8 years ago Loïc • 0
0
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2
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1.4k
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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
2.8 years ago rcreswell01 • 0
1
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3
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1.7k
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Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 2.9 years ago by 53k • written 2.9 years ago by ▴ 10
0
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1
reply
854
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DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 10
0
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0
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1.0k
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Job: Academic position in Non-clinical Biostatistics
JobPosting StatisticalMethod
3.1 years ago Laurent Gatto 1.6k
1
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2
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1.8k
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Limma adj.p.value the same for many different p.values
limmaGUI limma adj.p.value StatisticalMethod
3.2 years ago walkerrh95 • 0
0
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0
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1.4k
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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
3.3 years ago gaow • 0
0
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0
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848
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Should I adjust p value for multi-levels (groups) and multi-variables?
StatisticalMethod
3.7 years ago dong ▴ 10
2
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3
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6.2k
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Differential gene expression and (adjusted) p-values
edgeR StatisticalMethod
updated 3.6 years ago by • 0 • written 3.9 years ago by • 0
6
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4
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1.6k
views
Limma prametrization
limm MathematicalBiology limmaGUI StatisticalMethod
3.9 years ago Giovanni • 0
2
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7
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2.2k
views
EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on individual patients not combined
edgeR StatisticalMethod
4.3 years ago • updated 4.2 years ago Field -Ye • 0
0
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2
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2.2k
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To retrieve the transcript from gff file with the longest isoform
FunctionalAnnotation StatisticalMethod
4.5 years ago Aneesha • 0
0
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1
reply
1.2k
views
DESeq2 Design matrix
StatisticalMethod DESeq2
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
6
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6
replies
2.5k
views
limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 4.8 years ago by 53k • written 4.8 years ago by ▴ 10
1
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3
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1.7k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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0
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1.8k
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Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
4.9 years ago jol.espinoz ▴ 40
0
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2
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1.1k
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p adjusted value not available
StatisticalMethod DESeq2
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
29 results • Page 1 of 1
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Answer: segfault in edgeR glmQLFit by Gordon Smyth 53k
Dear Mark, Thank you for providing a reproducible example. I confirm that I can reproduce the segfault myself on my own computer. We will …
Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by aqeel • 0
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Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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
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