Showing : StatisticalMethod • reset
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 1 hour ago by ★ 4.1k • written 13 hours ago by • 0
2
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2
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623
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
3 months ago Linton • 0
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
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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
5 months ago Manthos • 0
4
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2
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DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
3
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670
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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
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deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
2
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4
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738
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Model comparison in mean-dispersion trend in DESeq2
DESeq2 StatisticalMethod
14 months ago Loïc • 0
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2
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732
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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
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3
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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 • 0
0
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DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 17 months ago by 41k • written 18 months ago by ▴ 10
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619
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Job: Academic position in Non-clinical Biostatistics
JobPosting StatisticalMethod
18 months ago Laurent Gatto 1.6k
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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
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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
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3
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3.2k
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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
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Should I adjust p value for multi-levels (groups) and multi-variables?
StatisticalMethod
2.1 years ago dong ▴ 10
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4
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985
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Limma prametrization
limm MathematicalBiology limmaGUI StatisticalMethod
2.3 years ago Giovanni • 0
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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
2.6 years ago Field -Ye • 0
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1.3k
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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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1
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732
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DESeq2 Design matrix
StatisticalMethod DESeq2
updated 3.0 years ago by 41k • written 3.0 years ago by • 0
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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 3.1 years ago by 50k • written 3.1 years ago by ▴ 10
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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
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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
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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
24 results • Page 1 of 1
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Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
> I am just re-processing due to being uncertain about how they used the edgeR analysis to reach gene level edgeR devs published something…
Comment: Differences in differential analysis methods for RNA-Seq by james.zhang20 • 0
Thanks for the explanations, it has helped clarify some things. Unfortunately, I am working from an early access public dataset (https://do…
Comment: Deseq2 and Normalization of RNA sequencing data by ATpoint ★ 4.1k
There is no expectation of normality that is realistic in terms of expression level. Levels are widely different between genes, and counts …
Comment: Differences in differential analysis methods for RNA-Seq by ATpoint ★ 4.1k
MAGeCK is a command line tool that is easy to use. I recommend you use it because a) the logFCs from DESeq2 and MAGeCK will be very similar…
Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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