How can I download Methylation data for MethylMix package. (unusual error popped)
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6 months ago

I am trying to use MethylMix package in R and do methylation analysis on the HNSC cancer data, from TCGA. I am doing this analysis on a remote server, from my home. Initially, I was able to run the Download_DNAmethylation() function and download the HNSC dataset directly from TCGA. After this step, I set this dataset to pre-processing. I used the function Preprocess_DNAmethylation(). It also started to run and took almost 2 days. Suddenly, it abruptly stopped, without any error displayed, and all the downloaded data also went away. I didn't understand what the issue was.

Anyways, I thought to repeat the other 2 processes again. Now, when I am entering the same command for downloading methylation HNSC data, it's showing an error.

METdirectories = Download_DNAmethylation(cancerSite, targetDirectory, downloadData = TRUE)

ERROR :-

Searching 27k MET data for: HNSC 
        There is no Merge_methylation__humanmethylation27 data for HNSC 
    Searching 450k MET data for: HNSC 
        There is no Merge_methylation__humanmethylation450 data for HNSC

However, earlier it used to start downloading the 450k MET data for : HNSC.

When I am executing the same set of commands in my local computer RStudio, then it is smoothly running the same set of commands and data is getting downloaded. Below is my entire code.

cancerSite = "HNSC"
targetDirectory = paste0(getwd(), "/")
METdirectories = Download_DNAmethylation(cancerSite, targetDirectory, downloadData = TRUE)
METProcessedData = Preprocess_DNAmethylation(cancerSite, METdirectories)

OUTPUT on local computer

Searching 27k MET data for: HNSC 
    There is no Merge_methylation__humanmethylation27 data for HNSC 
Searching 450k MET data for: HNSC 
    Downloading Merge_methylation__humanmethylation450 data, version: 20160128 
    This may take 10-60 minutes depending on the size of the data set.

Please help me out!

R software error MethylMix Methylation • 187 views
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