Showing : StatisticalMethod • reset
2
votes
2
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546
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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
1
vote
2
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417
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
3 months ago Sabiha ▴ 20
2
votes
2
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383
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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
4 months ago Manthos • 0
4
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2
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569
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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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654
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Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 9 months ago by 50k • written 9 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 • updated 13 months ago Loïc • 0
0
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2
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712
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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
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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
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1
reply
520
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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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591
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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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938
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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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858
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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
0
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0
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554
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Should I adjust p value for multi-levels (groups) and multi-variables?
StatisticalMethod
2.1 years ago dong ▴ 10
2
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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
6
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4
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966
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
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To retrieve the transcript from gff file with the longest isoform
FunctionalAnnotation StatisticalMethod
2.8 years ago Aneesha • 0
0
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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
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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
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 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: Error in champ.load(): The following specified files do not exist by Sherin • 0
it worked! thank you so much!!
Comment: Multi factor design edgeR/Deseq2 by Elizabeth • 0
Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…
Comment: DESeq2 setting significant p-value by Michael Love 41k
It does not resort. Also the dataset and results will have the same row names from object creation throughout the analysis.
Comment: Input Question for deseq.r by ATpoint ★ 4.0k
It is unclear what "deseq.r" is. It is not part of DESeq2, and almost certainly no part of RSeqAn. Please add details, and keep in mind tha…
Answer: DESEQ2 output gives multiple groups when only 2 groups are present by ATpoint ★ 4.0k
In the first PCA plot there is almost certainly some hidden character like whitespaces in the column from colData that encodes this group. …
Votes
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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