methylKit - calculate diff methylation

[Hongmei Li-Byarlay]

Hello,

I'm trying to calculate differential methylation from my triplicates (trt group has 3 replicates, and ctrl group has 3 replicates.) In order to test for differential methylation, I used the calculateDiffMeth as the documentation showed. 

myDiff=calculateDiffMeth(meth)

It showed msg as follow:

Error in .Method(..., na.last = na.last, decreasing = decreasing, method = method) : 

  'Calloc' could not allocate memory (938713 of 4 bytes)

In addition: Warning messages:

1: In doTryCatch(return(expr), name, parentenv, handler) :

  display list redraw incomplete

2: In doTryCatch(return(expr), name, parentenv, handler) :

  invalid graphics state

3: In doTryCatch(return(expr), name, parentenv, handler) :

  invalid graphics state

4: In doTryCatch(return(expr), name, parentenv, handler) :

  display list redraw incomplete

5: In doTryCatch(return(expr), name, parentenv, handler) :

  invalid graphics state

6: In doTryCatch(return(expr), name, parentenv, handler) :

  invalid graphics state

[Altuna Akalin]

how many CpGs do you have in your datasets? It seems that it's running out of memory

Best,

Altuna

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[Hongmei Li-Byarlay]

Each sample has 1,955,471 CG sites in average.

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[Altuna Akalin]

That shouldn't be a problem, could you send a reproducible example with a smaller dataset? Do the examples work ?

Best

Altuna

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