I downloaded the level 3 mRNA expression data TCGA-CESC project as expression estimates per gene from the GDC data portal with the TCGAbiolinks package. After that, I used TCGAbiolinks for preprocessing my data. In this way, TCGAanalyze_Normalization and TCGAanalyze_Filtering functions of the TCGAbiolinks package were used. Then I found DEGs between metastatic samples and primary tumors samples, now I want to use WGCNA for the construction of a gene co-expression network, how can I import RNAseq data to WGCNA?
Can I import the result of TCGAanalyze_Filtering to WGCNA?
And how can I download clinical metadata for my project? Because to relate co-expression modules to disease phenotypes, clinical metadata is needed.
Thanks in advance.