run only diff. methylation in RnBeads

[Catherina Romanova]

Hello everyone! 

I've run RnBeads analysis and after that I want to run methylation analysis separetely for different groups. But I don't wanna run all analysis, I want to use rnb.set object from previous! I tried something like that: rnb.set= load.rnb.set("/Projects/Killers/RnBeads/reports5/rnbSet_preprocessed/rnb.set.RData") and after that rnb.run.differential(rnb.set,report.dir), but I failed. Mb someone knows, how to load this object correctly?

thanx a lot!

[Yassen Assenov]

Hello Catherina,

Try:

rnb.set <- load.rnb.set("/Projects/Killers/RnBeads/reports5/rnbSet_preprocessed”)

Greetings,

Yassen

Hello everyone! 

I've run RnBeads analysis and after that I want to run methylation analysis separetely for different groups. But I don't wanna run all analysis, I want to use rnb.set object from previous! I tried something like that: rnb.set= load.rnb.set("/Projects/Killers/RnBeads/reports5/rnbSet_preprocessed/rnb.set.RData") and after that rnb.run.differential(rnb.set,report.dir), but I failed. Mb someone knows, how to load this object correctly?

thanx a lot!

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[Catherina Romanova]

Thank you for fast reply!

I did that, in this case I get an error  directory /Projects/Killers/RnBeads/reports8/differential_methylation_data can  not be created :(

понедельник, 27 августа 2018 г., 8:53:19 UTC+3 пользователь Yassen написал:

[Yassen Assenov]

So you managed to load the dataset. The problem is that a report on differential methylation already exists; RnBeads refuses to overwrite existing reports. You need to do one of the following:

1. Remove the existing directory (either everything in reports8, or at least all the files and subdirectories containing “differential” in their names), or

2. Specify another path in your R command, e.g. “/Projects/Killers/RnBeads/reports9”, and make sure the path does not exist.

Greetings,

Yassen

[Catherina Romanova]

Yes, you are right about directory, thank you! 

but after solving that I'm getting another error: Error in save.rnb.diffmeth(diffmeth, diffmeth.path) :

  trying to get slot "disk.dump" from an object of a basic class ("NULL") with no slots   and can't google it (

среда, 29 августа 2018 г., 23:34:50 UTC+3 пользователь Yassen написал:

Greetings,

Yassen

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[Catherina Romanova]

I suppose the problem was that in previous analysis I set another differential.comparison.columns. I tried previous columns, and it worked. 

пятница, 31 августа 2018 г., 17:00:11 UTC+3 пользователь Catherina Romanova написал: