I wish to download TCGA gene expression from XENA browser using the following link:
https://xenabrowser.net/datapages/?dataset=EB%2B%2BAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena&host=https%3A%2F%2Fpancanatlas.xenahubs.net&removeHub=http%3A%2F%2F127.0.0.1%3A7222
Yet they don't clearly mention what are the units and the normalization performed. All that is mentioned in units is log2(norm_value+1) and its unclear what is this norm_value. is it RSEM, TPM or FPKM?
If anyone knows and can point me out to a resource that explains how their normalization was performed it would be very much appreciated
The TCGA gene expression units in the PANCAN batch effects normalized gene expression data available on the Xena browser are in the form of log2-transformed normalized expression values, where the normalization method used is not explicitly stated.
The normalization method used for the EB++AdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.xena dataset is not specified on the Xena browser website. However, based on the description of the normalization units, it is possible that the normalization was performed using the log2(TPM+1) or log2(FPKM+1) method.
The normalization units, log2(norm_value+1), suggest that the data may have been normalized using a method that produces values similar to TPM or FPKM. The "+1" is added to the value to avoid taking the log of zero, which can cause errors in downstream analysis.
To get more information on the normalization method used, you can try contacting the TCGA or Xena browser support team for more details. Alternatively, you can check the original publications or data sources for the dataset to see if the normalization method is explicitly stated there.
Which publication should mention how Xena browser performed their normalization and the batch control?
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