I'm trying to establish prognostic biomarkers and I have used the GSE53757 dataset for the same. I'm done with DEA and WGCNA and I obtained 52 genes that corresponded to the pathway i wanted to study. I need to perform regression analysis on these 52 genes and I have used the TCGA dataset to perform regression analysis and obtained results. In order to validate my regression analysis I need to perform it on the GSE53757 dataset as well. But when analysing the phenoData and the featureData for the GSE53757 dataset I could not find any data for patient survival and I'm not able to contact the authors who have uploaded the dataset. What should I do? Also I cannot change the dataset I'm currently working on
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I'm trying to establish prognostic biomarkers and I have used the GSE53757 dataset for the same. I'm done with DEA and WGCNA and I obtained 52 genes that corresponded to the pathway i wanted to study. I need to perform regression analysis on these 52 genes and I have used the TCGA dataset to perform regression analysis and obtained results. In order to validate my regression analysis I need to perform it on the GSE53757 dataset as well. But when analysing the phenoData and the featureData for the GSE53757 dataset I could not find any data for patient survival and I'm not able to contact the authors who have uploaded the dataset. What should I do? Also I cannot change the data-+\set I'm currently working on
Copilot said
It sounds like you've hit a bit of a roadblock with missing survival data in the GSE53757 dataset. Since you can't change the dataset, here are a few options to navigate this challenge:
To summarize your situation:
The GSE53757 dataset (kidney tumor–related microarray data) does not contain clinical survival information (such as OS or DFS), which fundamentally prevents direct Cox regression or Kaplan–Meier validation. Since contacting the authors is not possible and the dataset itself cannot be changed, the methodological options are limited.
It is possible, however, to use proxy endpoints for validation.
GSE53757 contains information such as tumor vs. normal, stage, grade, and metastasis status. As a proxy for survival, regression or ROC analysis using these clinical outcomes (especially stage/grade) can be performed to support and strengthen the results.
Finally, this limitation should be explicitly stated in the manuscript. For example:
“Although GSE53757 was used for validation, survival data were not available; therefore, validation of survival analysis relied on internal cross-validation within TCGA.”
“In GSE53757, indirect support was provided by demonstrating associations between gene expression and tumor vs. normal tissue, or disease stage.”
This would be a realistic way to present the limitation.
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