Bioconductor Complex-design

Showing : complex-design • reset

votes

replies

1.4k

views

limma complex-design paired design

updated 6.8 years ago by Aaron Lun ★ 28k • written 6.8 years ago by ML18 ▴ 10

votes

replies

2.6k

views

rnaseqpower sspa sample size sequencing complex-design

updated 8.8 years ago by m.van_iterson ▴ 20 • written 8.9 years ago by roser.navarro • 0

votes

replies

6.0k

views

limma paired samples complex-design

9.0 years ago • updated 8.9 years ago aec ▴ 90

votes

replies

4.3k

views

limma model matrix limma design matrix complex-design

updated 9.5 years ago by Aaron Lun ★ 28k • written 9.5 years ago by Guido Hooiveld ★ 4.1k

vote

3.1k

views

deseq2 multiple factor design complex-design

updated 9.8 years ago by Michael Love 43k • written 9.8 years ago by sifujio • 0

vote

replies

7.0k

views

combat software error rnaseq complex-design

updated 10.2 years ago by Peter Langfelder ★ 3.0k • written 10.2 years ago by Stefano Mangiola ▴ 20

votes

replies

2.6k

views

edgeR complex-design

updated 10.2 years ago by James W. MacDonald 67k • written 10.2 years ago by lwc628 ▴ 20

7 results • Page 1 of 1

Recent ...

Replies

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

Awards • All