Normal sample as controls about mnp_training HOT 1 CLOSED

Hi,

1. and 2. I was not able to gather all the raw idat files of the 100 normal control samples, because many of them were taken from a minif RGset available in this Bioconductor-package

https://bioconductor.org/packages/3.4/data/experiment/html/CopyNumber450kData.html

We do not own the idat files and the CopyNumber450kData package is outdated so that you need to downgrade your minfi package to access the data.

To make things more simple, I have uploaded our conumee reference objects with the 50 female and 50 male samples as well as the annotation object that we use. Together with these you should be able to follow the steps in the newly uploaded R script cnv_analysis.R to generate the same CNV plots that we presented in the manuscript.

To download the reference objects you need Git large file storage installed:

https://git-lfs.github.com/

and then simply clone the repo:

git clone https://github.com/mwsill/mnp_training.git

3. FFPE == DNA_FFPE and DNA_KRYO == Frozen

Best,

Martin

from mnp_training.