Showing : StatisticalMethod • reset
2
votes
2
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618
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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
replies
448
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
2
votes
2
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400
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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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614
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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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2
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669
views
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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4
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736
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Model comparison in mean-dispersion trend in DESeq2
DESeq2 StatisticalMethod
14 months ago Loïc • 0
0
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2
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730
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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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902
views
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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1
reply
528
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DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 17 months ago by 41k • written 18 months ago by ▴ 10
0
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0
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615
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Job: Academic position in Non-clinical Biostatistics
JobPosting StatisticalMethod
18 months ago Laurent Gatto 1.6k
1
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2
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964
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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
0
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0
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879
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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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562
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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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3.2k
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Differential gene expression and (adjusted) p-values
edgeR StatisticalMethod
updated 24 months ago by • 0 • written 2.3 years ago by • 0
6
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4
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984
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Limma prametrization
limm MathematicalBiology limmaGUI StatisticalMethod
2.3 years ago Giovanni • 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
0
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2
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1.3k
views
To retrieve the transcript from gff file with the longest isoform
FunctionalAnnotation StatisticalMethod
2.9 years ago Aneesha • 0
0
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1
reply
732
views
DESeq2 Design matrix
StatisticalMethod DESeq2
updated 3.0 years ago by 41k • written 3.0 years 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 3.1 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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722
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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
Recent ...
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Answer: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by James W. MacDonald 65k
You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…
Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Votes
SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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