Hello,
Thank you very much for sharing the scripts to adjust the beta values according to the purity of the samples.
I am trying to adjust the Beta values of my Illumina EPIC microarray from Formalin-Fixed Paraffin-Embedded (FFPE) tissue specimens from lung cancer.
Unfortunately, I had this error: Error in checkForRemoteErrors(val) :
one node produced an error: unable to find an inherited method for function ‘getModel’ for signature ‘"flexmix"’.
This issue seems to be linked to the beta values of certain CpGs of my dataset. In fact, even when I create a smaller dataset by filtering the first 1000 lines, the problem persists. However, upon removing the CpG responsible for the issue, the problem resolves. Additionally, I observed that rounding the beta values of the problematic CpG also resolves the issue.
When I compare the problematic CpG with the others that are functioning properly, I don’t see any difference.
I tried also to run the tcgaBRCA dataset, everything works well.
I don't understand what is wrong with my dataset. Could you kindly help me in understanding the reason of this problem? This is the first time I need to adjust the beta values according to the purity of the samples.
Thank you in advance.
Best regards,
Luca
Hello,
Thank you very much for sharing the scripts to adjust the beta values according to the purity of the samples.
I am trying to adjust the Beta values of my Illumina EPIC microarray from Formalin-Fixed Paraffin-Embedded (FFPE) tissue specimens from lung cancer.
Unfortunately, I had this error: Error in checkForRemoteErrors(val) :
one node produced an error: unable to find an inherited method for function ‘getModel’ for signature ‘"flexmix"’.
This issue seems to be linked to the beta values of certain CpGs of my dataset. In fact, even when I create a smaller dataset by filtering the first 1000 lines, the problem persists. However, upon removing the CpG responsible for the issue, the problem resolves. Additionally, I observed that rounding the beta values of the problematic CpG also resolves the issue.
When I compare the problematic CpG with the others that are functioning properly, I don’t see any difference.
I tried also to run the tcgaBRCA dataset, everything works well.
I don't understand what is wrong with my dataset. Could you kindly help me in understanding the reason of this problem? This is the first time I need to adjust the beta values according to the purity of the samples.
Thank you in advance.
Best regards,
Luca