Question: Error while using ChAMP
0
gravatar for halo22
2.3 years ago by
halo22120
Indianapolis, IN
halo22120 wrote:

Hello All,

I am using ChAMP do run a methylation analysis on the 450k dataset. I am not running every step individually but using the champ.process function to run the entire pipeline just by providing location to my IDAT directory which has my the sample_sheet.csv file. The program does run for a while, it produces the CHAMP_RESULTS directory and few other files but dies at or during normalization. Below is the a snippet of my error log file. Could you please tell me what happening here and is there a way to fix this?

Running champ.norm()...

[===========================]

[>>>>> ChAMP.NORM START <<<<<<]


champ.norm Results will be saved in ./CHAMP_RESULT//CHAMP_Normalization/

[ SWAN method call for BOTH rgSet and mset input, FunctionNormalization call for rgset only , while PBC and BMIQ only needs beta value. Please set parameter correctly. ]

<< Normalizing data with BMIQ Method >>

Note that,BMIQ function may fail for bad quality samples (Samples did not even show beta distribution).

3 cores will be used to do parallel BMIQ computing.

Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, :

internet routines cannot be loaded

Calls: champ.process ... makePSOCKcluster -> newPSOCKnode -> socketConnection

Execution halted

methylation bioconductor R 450k • 896 views
ADD COMMENTlink written 2.3 years ago by halo22120
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