Hello,

I have downloaded the TCGA data from cBioPortal. I would like to know about ‘data_RNA_Seq_v2_expression_median’. I see the values are RSEM.

Hugo_Symbol    TCGA-2V-A95S-01  TCGA-2Y-A9GS-01    TCGA-2Y-A9GT-01
UBE2Q2P3                1.5051       26.412                0
UBE2Q2P3                3.7074       2.6663              4.4833
LOC149767              90.1124       71.0054             95.5122
TIMM23                1017.1038      639.2311           742.4344
MOXD2                     0            0                    0
LOC155060              141.3911      22.7206              95.046
LOC100132347          1285.5514     1281.4194            535.306
EFCAB12                20.1987        27.5998            151.5355
LOC147680             22282.261     22641.9271           77669.9484
  A1CF                583.1569      1572.6959            1280.4304

I would like to identify differential expressed genes with this data. Do I need to transform the data before differential analysis? Which package would be useful for this? BTW I also see that cBioportal has z-scores. Are there any packages to do differential analysis with z-scores?

Thank you