I would need to retrieve the normalisation (and maybe the batch correction method) used to produced the pan-Cancer Atlas mRNA expression matrix (file called 'EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv' found [here][1]).

Starting from the raw read counts obtained from the GDC and the same gene panel, I tried FPKM and FPKM-UQ normalisation as described [here][2], but the expression values obtained do not fall at all in the same range as in the pan-Cancer mRNA matrix. Maybe that would suggest a cross-sample batch correction.

My goal is, starting from raw read counts, to normalise expression data from new samples together with the pan-Cancer mRNA data, in order to get a unified expression matrix and to be able to compare apples to apples basically.

Any information or alternative method would be greatly appreciated.



  [1]: https://gdc.cancer.gov/about-data/publications/PanCanStemness-2018
  [2]: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#mrna-expression-workflow
My guess (and it is only a guess), given the name of the file, that this is build from the RSEM quantification results that are present in the Broad Institute's [Firehose porta][1]l, rather than from read counts. 

RSEM use an EM algorithm to build isofrom expression values. A length-weighted sum of these values is then used to create gene expression values. 

The firehose documentation states that these are normalised like so:

> RSEM expression estimates are normalized to set the upper quartile
> count at 1000 for gene level and 300 for isoform level estimates.

Please note that this is definately NOT a batch correction and that [batch effects have been shown to be a serious problem with PanCancer analyses][2] (although this is at the level of somatic variants)


  [1]: https://gdac.broadinstitute.org/
  [2]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5387285/