Hi! I'm very new to the bioinformatics scene and need advice on a project. One of the initial steps is to compare the deconvolution results of normal and tumor tissue RNA-seq (TPM) data from GTEx and TCGA (specifically ovarian cancer data), but I am confused about how to go about normalization and batch effect correction prior to doing this.
I am planning to use limma as mentioned by many papers I have found. However, I am still confused as to whether this is appropriate for my project, especially since I have seen posts online discouraging the use of TPM data.
How can I ensure that my normal and tumor tissue data are properly normalized / corrected for batch effects before running them through CIBERSORTx?