How do I remove duplicate samples from a KM plot?
If your plot has an '!' icon next to the p-value this means that some patients are in your plot twice. This can happen when A) a patient has both a tumor and normal sample or when a patient has a metastasis that is part of the dataset and/or B) a tumor sample was split into multiple aliquots and then run through the same analysis twice.
- 1.Add the data column of 'sample type' from the Phenotype data
2. Filter to only samples that are 'Primary tumor' by typing 'primary' into the filter search box. Next, click the filter icon next to the filter search box and chose 'Filter'. This will filter out all samples that are not primary tumor.
3. Run your KM analysis by clicking the caret menu at the top of the column and choosing 'Kaplan-Meier plot' It will now only have primary tumor samples in it.
Removing duplicate samples from TCGA Lower Grade Glioma KM analysis