How to 'force=TRUE' in Human Methylation BeadChip module

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1

Hello everybody,

I am very new to Galaxy and hope for help with a - most likely - very trivial problem. I am trying to run the Infinium Human Methylation BeadChip module according to the respective Tutorial but using my own data. Unfortunately, I now encountered the error:

“(…)
Error in read.metharray(list.files(pattern = “_Red.idat”)) :
[read.metharray] Trying to parse IDAT files with different array size but seemingly all of the same type.
You can force this by ‘force=TRUE’, see the man page ?read.metharray
Execution halted”

According to what I found in the Bioconductor forum, this seems to happen quite regularly with EPIC data and it should be okay to try the ‘force=TRUE’. But, unfortunately, I do not know how to adjust this setting using Galaxy.

Any advice would be very welcome!

Many thanks in advance and best wishes,
Lea

2

Hi @ljflitsch,
I opened a PR in order to include this option in the Galaxy wrapper.

Regards

3

Hey,
@gallardoalba: Thank you very much for your help and effort. Since I am really new to this topic: Is there any way to get notified once this option becomes actually usable in Galaxy as an ‘end user’? E.g. anything/anywhere I can ‘follow’ to receive updates on this matter (perhaps via registering at GitHub)? Sorry for any inconveniences and best regards!

4

Yes, if you leave a comment in the PR, it will notify the news related to it.

Regards

5

Will do so. Thank you very much.

6

Are there perhaps any news on this topic? It has been a while since this help request and the corresponding PR has been initiated. Unfortunately though, I’m still encountering the same error message I’ve also had back then. Thus, I am now wondering whether the error might originally have had a different source or whether the ‘force=TRUE’ option was not yet included in the Galaxy wrapper (at least I could not spot a new setting bar for this). Many thanks!

7

Hi @ljflitsch,
sorry, I didn’t get any response from the tool developers; I tried again to ask them to review the Pull Request. If in the next few days there’re no news, I’ll try to find a different solution.

Regards