Charles Warden

The requested end date to work in the Integrative Genomics Core at City of Hope for the developer (Charles Warden) is 4/30/2024, where he will then enroll in the "Genetics, Genomics, and Bioinformatics" PhD program at UC-Riverside. While some support was provided when he was at the University of Michigan, there was discussion about how the transition plan could be improved during this time of change. After discussions, the decision was made to actively request that the Bioconductor version be retired,...

Hi Diraj, I have started a GitHub issue for the topic of parameter troubleshooting: https://github.com/cwarden45/COHCAP/issues/4 Please continue the discussion on GitHub. Thank you very much for your interest in using COHCAP! Sincerely, Charles

I have now made the following modifications in the sample description file: 1) I replaced spaces with underscores (in the group names). 2) I have removed all of the "Solid Tissue Normal" samples, so that only 2 groups exist when trying to run a 2-group comparison. While the non-primary sample count is much smaller, I was guessing you might want to look at a metastatic or recurrent group if you were defining the primary tumor as the reference. For example, in a tumor versus normal comparison, the...

I have now made the following modifications in the sample description file: 1) I replaced spaces with underscores (in the group names). 2) I have removed all of the "Solid Tissue Normal" samples, so that only 2 groups exist when trying to run a 2-group comparison. While the non-primary sample count is much smaller, I was guessing you might want to look at a metastatic or recurrent group if you were defining the primary tumor as the reference. For example, in a tumor versus normal comparison, the...

I have now made the following modifications in the sample description file: 1) I replaced spaces with underscores (in the group names). 2) I have removed all of the "Solid Tissue Normal" samples, so that only 2 groups exist when trying to run a 2-group comparison. While the non-primary sample count is much smaller, I was guessing you might want to look at a metastatic or recurrent group if you were defining the primary tumor as the reference. For example, in a tumor versus normal comparison, the...

I have now made the following modifications in the sample description file: 1) I replaced spaces with underscores (in the group names). 2) I have removed all of the "Solid Tissue Normal" samples, so that only 2 groups exist when trying to run a 2-group comparison. While the non-primary sample count is much smaller, I was guessing you might want to look at a metastatic or recurrent group if you were defining the primary tumor as the reference. For example, in a tumor versus normal comparison, the...

I have now made the following modifications in the sample description file: 1) I replaced spaces with underscores (in the group names). 2) I have removed all of the "Solid Tissue Normal" samples, so that only 2 groups exist when trying to run a 2-group comparison. While the non-primary sample count is much smaller, I was guessing you might want to look at a metastatic or recurrent group if you were defining the primary tumor as the reference. For example, in a tumor versus normal comparison, the...

I have now made the following modifications in the sample description file: 1) I replaced spaces with underscores. 2) I have removed all of the "Solid Tissue Normal" samples, so that only 2 groups exist when trying to run a 2-group comparison. While the non-primary sample count is much smaller, I was guessing you might want to look at a metastatic or recurrent group if you were defining the primary tumor as the reference. For example, in a tumor versus normal comparison, the normal group would be...