I am studying computational methods related to microRNAs to identify their diagnostic and therapeutic ability at the presence of prostate cancer. I have planned to analyse the TCGA PRAD data and want to get a clear idea about fundamental steps of TCGA analysis from raw data (Ex: Extraction, Processing, Normalisation, etc). I am grateful for your valuable opinions and recommendations with a concrete example.
Thank You!
Hi
You can download the level 3 data from dataportal of TCGA offical website or other website (FIREHOSE, UCSC CANCER BROWSER). I recommend that you can choose the latter two websites to download the level 3 data, because the gene expression matrix was processed and merged. However, the data from dataportal is separated (each patient has one gene expression file), and You need to merge these files using the Perl. In addition, the level 3 data is counts files And can be normalized by the R package "DESeq2" or "edgER". Then, you can perform differential expression (DE) analysis to identify DE genes.
With regards
Yuan-Bo Pan Thank You very much for your response. I will follow up the steps.
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