Blog: Fundamental Analysis of TCGA RNA-seq Data-02
This is the second part of the overall analysis pipeline, mainly documenting how to download and process data.
Data Selection
I would like to compare the gene differential expression (DE) between tumor and tumor_matched_normal (TN) samples
For speeding up the analysis, firstly I chose ACC (Adrenocortical carcinoma) which is the first item in Firehose, only contains 92 samples. However, there is no TN data inside
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The overall post is here: Fundamental Analysis of TCGA RNA-seq Data-02
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Please don't break these into multiple posts. When you are ready, do a single post and include links to your blog, which would be easy to work through.
OK, that would be better.
Since you are dealing with clinical sequencing data, would you mind posting model building (using ANCOVA), model evaluation (internal performance by loocv or any other method with confusion matrix), prediction using an independent set, followed by auc? Thanks in advance:)
Sorry, I cant follow you...
Sorry to separate the posts! I have made the post compilation here: Post Series: Fundamental Analysis of TCGA RNA-seq Data