Showing : StatisticalMethod • reset
2
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Differential gene expression and (adjusted) p-values
edgeR StatisticalMethod
updated 2.0 years ago by • 0 • written 2.3 years ago by • 0
2
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3
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1.9k
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deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 13 months ago by ★ 4.1k • written 14 months ago by • 0
6
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6
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1.7k
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limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 3.2 years ago by 50k • written 3.2 years ago by ▴ 10
2
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7
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1.5k
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EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on individual patients not combined
edgeR StatisticalMethod
2.7 years ago Field -Ye • 0
0
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2
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1.4k
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To retrieve the transcript from gff file with the longest isoform
FunctionalAnnotation StatisticalMethod
2.9 years ago Aneesha • 0
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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
1
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3
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1.1k
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How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
6
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4
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1.0k
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Limma prametrization
limm MathematicalBiology limmaGUI StatisticalMethod
2.3 years ago Giovanni • 0
1
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2
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988
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Limma adj.p.value the same for many different p.values
limmaGUI limma adj.p.value StatisticalMethod
19 months ago walkerrh95 • 0
1
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3
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938
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Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 15 months ago by 50k • written 15 months ago by ▴ 10
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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
20 months ago gaow • 0
2
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4
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756
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Model comparison in mean-dispersion trend in DESeq2
DESeq2 StatisticalMethod
15 months ago Loïc • 0
0
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2
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755
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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
15 months ago rcreswell01 • 0
0
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1
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744
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DESeq2 Design matrix
StatisticalMethod DESeq2
updated 3.0 years ago by 42k • written 3.0 years ago by • 0
0
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2
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740
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p adjusted value not available
StatisticalMethod DESeq2
updated 3.5 years ago by ★ 3.9k • written 3.5 years ago by • 0
2
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2
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712
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
4 months ago Linton • 0
3
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2
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688
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 11 months ago by 50k • written 11 months ago by ▴ 10
4
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2
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675
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DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
0
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648
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Job: Academic position in Non-clinical Biostatistics
JobPosting StatisticalMethod
18 months ago Laurent Gatto 1.6k
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576
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Should I adjust p value for multi-levels (groups) and multi-variables?
StatisticalMethod
2.2 years ago dong ▴ 10
0
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1
reply
543
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DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 17 months ago by 42k • written 18 months ago by ▴ 10
1
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2
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495
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago • updated 4 months ago Sabiha ▴ 20
2
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2
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438
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DESeq2: Comparison of single clinical sample to 4 normals using tumour cohort to infer dispersion of single sample
GeneExpression DESeq2 RNASeqData RNASeq StatisticalMethod
6 months ago • updated 5 months ago Manthos • 0
0
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3
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224
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 16 days ago by ★ 4.1k • written 17 days ago by • 0
24 results • Page 1 of 1
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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