Bug: for R ChAMP package

Question

[Shicheng Guo]

I think I found a bug in the R package of "ChAMP". Even In its latest version, this bug were still existed there. As the following code shown in line 237 of function champ.lasso,

myDf <- data.frame(myDf, dmr.beta.means[,22:24])  #

Actually, I think it should be

myDf <- data.frame(myDf, dmr.beta.means[,17:19])  #

That's my opinion, I have contact the authors, However, there is no any response for long time. Is there any other friend found this problem/bug?

A: Package can be found here: http://www.bioconductor.org/packages/devel/bioc/html/ChAMP.html

[Devon Ryan]

Please post this on the bioconductor support site.

[Shicheng Guo]

it is very interesting. bioconductor support site use same frame of the web building with biostars. Do they have same CEO or CTO?

[Devon Ryan]

The framework for the site is an open source project that a number of sites use (there's also a neurostars and a swedish bioinformatics site that use the same framework). There are no shared people between the two sites that I know of (this one is run by Istvan, the bioconductor site is probably run by the bioconductor core team (I assume).

[Shicheng Guo]

Hey Devon, Just wondering how to get the source of the framework like biostars, bioconductor support site.

[Devon Ryan]

It's on github :)

Answer 1

[champ450k]

Hi Shicheng,

Thank you for your question. This update has been submitted and should be available from Bioconductor by the end of the week.

Best wishes
Tiffany