Altuna Akalin

I don't think we can deal with that case. Covariates shouldn't have missing data probably if I'm not mistaken. On Fri, Sep 17, 2021 at 11:23 PM TYRANISTAR ***@***.***> wrote:...

Hi Marcin, I don't follow google's R style guide, and probably will not follow it in the future. Unless Bioconductor demands that I use it, I will not change these....

I think there is a misunderstanding about what simulation means or how to use it. Please see https://github.com/BIMSBbioinfo/Strategies_for_analyzing_BS-seq and the associated paper to understand how it is used. On Sun,...

I think you have to use assocComp and see if the sequencing batch effect string correlates with one of the PCs, try to remove that component. There is no function...

It seems PCs are not strongly associated with the batch, you might have other covariates you don’t know about that might explain the PCA plot. Best Altuna On Wed, Dec...

Check discussion forum, I have answered this question many times. short answer: there are possible routes to take, we don’t have any code for those possible routes Best Altuna On...

I think this should be a additional feature, we shouldn't force users to have seqlengths in their GRanges objects. I guess we are on the same page on this, but...

could you send a reproducible example, it doesn't have to be the full example. It just has to exemplify the memory problem. we have to do some sort of memory...

this is because is.noCovNA is not designed to deal with negative values, and designed with methylation values in mind. Although, for ChIP-seq FCs it may not make sense to use...

this could be due the new object being a vector, [,drop=FALSE] should be used somewhere in that code maybe On Mon, Nov 21, 2016 at 2:51 PM, frenkiboy [email protected] wrote:...