Showing : StatisticalMethod • reset
3
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p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 11 weeks ago by • 0 • written 3 months ago by • 0
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241
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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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458
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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
730
views
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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0
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625
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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
18 months ago pierre.devillemereuil • 0
0
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3
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1.4k
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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
23 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
2.0 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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847
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DESeq2 paired multifactor test
DESeq2 StatisticalMethod
updated 3.0 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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1.7k
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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
3.2 years ago gaow • 0
0
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0
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844
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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
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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
4.2 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
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1.2k
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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 4.7 years ago by 53k • written 4.7 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
Recent ...
Replies
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…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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
Awards • All
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