[BioC] Question about Diffbind input control

[Rory Stark]

Hi Anna-

Before running DESeq, DiffBind sets all counts to a minimum value of 1.
Not sure if that is in the documentation anywhere!

Cheers-
Rory

On 11/09/2013 17:47, "Anna Poetsch" <Anna.Poetsch at cancer.org.uk> wrote:

>Dear Rory,
>
>I attended the class about ChIP-Seq data analysis at EBI recently, where
>you introduced us to the Diffbind package. There is still something that
>I do not quite understand. It is about the correction for Input reads:
>How is the correction for input done? Are the input counts just
>subtracted after normalisation? If so, how does the package deal with
>resulting negative counts, which would not be accepted by DESeq? Since
>there is a normalisation step in between, the counts would not be
>integers anymore, but DESeq needs integers. How is this solved?
>I really tried to solve these questions looking at all the documentation
>I could find and tried but failed to understand the source code. It would
>be really nice, if you could help me with this.
>
>Kind regards,
>Anna Poetsch