Entering edit mode
6.6 years ago
Biologist
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290
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