Showing : StatisticalMethod • reset
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 3.1 years ago by 50k • written 3.2 years ago by ▴ 10
6
votes
4
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988
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Limma prametrization
limm MathematicalBiology limmaGUI StatisticalMethod
2.3 years ago Giovanni • 0
4
votes
2
replies
630
views
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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2
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674
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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
2
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3
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1.8k
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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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3
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3.2k
views
Differential gene expression and (adjusted) p-values
edgeR StatisticalMethod
updated 2.0 years ago by • 0 • written 2.3 years ago by • 0
2
votes
4
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741
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Model comparison in mean-dispersion trend in DESeq2
DESeq2 StatisticalMethod
14 months ago Loïc • 0
2
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7
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1.5k
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
2
votes
2
replies
634
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
4 months ago • updated 3 months ago Linton • 0
2
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2
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408
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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
1
vote
3
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911
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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
1
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2
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463
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
1
vote
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
1
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2
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966
views
Limma adj.p.value the same for many different p.values
limmaGUI limma adj.p.value StatisticalMethod
19 months ago walkerrh95 • 0
0
votes
3
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118
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 2 days ago by ★ 4.1k • written 3 days 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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0
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625
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Job: Academic position in Non-clinical Biostatistics
JobPosting StatisticalMethod
18 months ago Laurent Gatto 1.6k
0
votes
2
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1.4k
views
To retrieve the transcript from gff file with the longest isoform
FunctionalAnnotation StatisticalMethod
2.9 years ago Aneesha • 0
0
votes
1
reply
530
views
DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 17 months ago by 41k • written 18 months ago by ▴ 10
0
votes
1
reply
735
views
DESeq2 Design matrix
StatisticalMethod DESeq2
updated 3.0 years ago by 41k • written 3.0 years ago by • 0
0
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2
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737
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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
0
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0
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565
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Should I adjust p value for multi-levels (groups) and multi-variables?
StatisticalMethod
2.1 years ago dong ▴ 10
0
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0
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888
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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
votes
2
replies
724
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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
24 results • Page 1 of 1
Recent ...
Replies
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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