Showing : StatisticalMethod • reset
3
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p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 3 months ago by • 0 • written 4 months ago by • 0
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248
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Correlation threshold
MethylationArray methylationArrayAnalysis StatisticalMethod
8 months ago user_bioinfo • 0
1
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2
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469
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Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData signatureSearchData StatisticalMethod
written 12 months ago by • 0
0
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1
reply
734
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Can we compare 3 different experimental conditions with DESeq2?
DESeq2 StatisticalMethod
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
0
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Job: Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL
StatisticalMethod Evolution QuantitativeTrailLocus Genetics JobPosting
19 months ago pierre.devillemereuil • 0
0
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3
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1.5k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
2
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2
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DESeq2 median of ratios normalization instead of VST or rlog for ordinations?
DESeq2 medianofratiostransformation StatisticalMethod Normalization dispersion
23 months ago Linton • 0
1
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2
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1.3k
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How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
24 months ago Sabiha ▴ 20
2
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2
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1.1k
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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
2.1 years ago Manthos • 0
5
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2
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2.2k
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DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 2.1 years ago by 53k • written 2.1 years ago by ▴ 10
3
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2
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1.2k
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Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 30
2
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3
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3.7k
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deseq2 normalization and statistical method
normalization deseq2 StatisticalMethod
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
2
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4
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1.2k
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Model comparison in mean-dispersion trend in DESeq2
DESeq2 StatisticalMethod
2.8 years ago Loïc • 0
0
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2
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1.4k
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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
2.8 years ago rcreswell01 • 0
1
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3
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1.7k
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Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 2.9 years ago by 53k • written 2.9 years ago by ▴ 10
0
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1
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854
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DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 3.1 years ago by 43k • written 3.1 years ago by ▴ 10
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0
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1.0k
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Job: Academic position in Non-clinical Biostatistics
JobPosting StatisticalMethod
3.1 years ago Laurent Gatto 1.6k
1
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2
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1.8k
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Limma adj.p.value the same for many different p.values
limmaGUI limma adj.p.value StatisticalMethod
3.2 years ago walkerrh95 • 0
0
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0
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1.4k
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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
3.3 years ago gaow • 0
0
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0
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848
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Should I adjust p value for multi-levels (groups) and multi-variables?
StatisticalMethod
3.7 years ago dong ▴ 10
2
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3
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6.2k
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Differential gene expression and (adjusted) p-values
edgeR StatisticalMethod
updated 3.6 years ago by • 0 • written 3.9 years ago by • 0
6
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4
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1.6k
views
Limma prametrization
limm MathematicalBiology limmaGUI StatisticalMethod
3.9 years ago Giovanni • 0
2
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7
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2.2k
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EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on individual patients not combined
edgeR StatisticalMethod
4.3 years ago • updated 4.2 years ago Field -Ye • 0
0
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2
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2.2k
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To retrieve the transcript from gff file with the longest isoform
FunctionalAnnotation StatisticalMethod
4.5 years ago Aneesha • 0
0
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1
reply
1.2k
views
DESeq2 Design matrix
StatisticalMethod DESeq2
updated 4.6 years ago by 43k • written 4.6 years ago by • 0
6
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6
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2.5k
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limma:arrayWeights() and the "prior.n" parameter for biological replicates? (PROTEOMICS)
Proteomics limma StatisticalMethod
updated 4.8 years ago by 53k • written 4.8 years ago by ▴ 10
1
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3
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1.7k
views
How to assign random effect factor in DESeq2 desing?
StatisticalMethod DESeq2 phyloseq
updated 4.8 years ago by 43k • written 4.8 years ago by • 0
0
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0
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1.8k
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Why is `scale-free topology` estimated as -sign(slope) * (R^2) in WGCNA?
Network StatisticalMethod WGCNA ExpressionData
4.9 years ago jol.espinoz ▴ 40
0
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2
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1.1k
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p adjusted value not available
StatisticalMethod DESeq2
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by • 0
29 results • Page 1 of 1
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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