cancer type prediction based on RNASeq gene expression data?
Hi,
I have several RNASeq data from FFPE, which were collected from several patients with cancer of unknown primary.
I processed the RNASeq data using STAR or hisat2, and convert the bam to FPKM or FPKM_UQ gene expression matrix.
TULIP was applied to predict the cancer type based on the expression data.
However, unexpected errors went out, either with FPKM or FPKM_UQ values.
I am wondering is there any other popular tool that can be applied on the expression data or the raw data(bam)?
Best,
Junfeng
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Just to be sure: are all the metastatic samples collected from the same organ? As: secondary tumors found in lungs with unknown origin? Patients with the same sex?
all the samples are not metastatic.
For TULIP, I downloaded a sample FPKM_UQ value from GDC, and encountered the same error report from the tool. I've contact the author, hope the bug can be fixed.