I want to prepare a matrix of gene expression to analyse TCGA LAML data.

The required data is available at TCGA LAML - Gene expression quantification.

The following is an example of the kind of data retrieved from the TCGA data portal:

ENSG00000000003.13  9
ENSG00000000005.5   1
ENSG00000000419.11  661
ENSG00000000457.12  1434
ENSG00000000460.15  1211
ENSG00000000938.11  405
ENSG00000000971.14  251
ENSG00000001036.12  786
ENSG00000001084.9   4423
ENSG00000001167.13  5038
ENSG00000001460.16  246
ENSG00000001461.15  2773
ENSG00000001497.15  1932
ENSG00000001561.6   1693
ENSG00000001617.10  55
ENSG00000001626.13  8
ENSG00000001629.8   4629

Each row displays, for each gene, the quantification of read counts by the htseq tool.

My question is, how do I have to preprocess the data (e.g. regarding gene length) before using data for subsequent analysis?

In this case I will not consider normalisation (such as loess) and batch effects removal (e.g. with combat).


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