Showing : design formula • reset
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Understanding interaction term in DESeq2
deseq2 design formula log fold change
updated 4 months ago by 43k • written 4.4 years ago by ▴ 40
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DESeq2 design formula
deseq2 design formula
updated 4.9 years ago by ★ 1.4k • written 4.9 years ago by • 0
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Time series experiment analysis in DEseq2 without T=0 and three independent experiments with linked samples
deseq2 rnaseq repeated measures time series design formula
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 10
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Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
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Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2 design formula design matrix edgeR ATAC
updated 5.0 years ago by 52k • written 5.0 years ago by • 0
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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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