Hello, I am very new to RNA-seq data and have no bioinformatics background. I have downloaded the TCGA data from cBioPortal. I would like to know about ‘data_RNA_Seq_v2_expression_median’. I presume they are absolute expression values. Why is it that for some tumors, the values are zero?
Can these values be converted to log scale for comparison of expression between different histologic subtypes of tumors (as for microarrays)? I would like to identify differentially expressed genes and generate heat maps from the expression data. How do I go about it and which software would be useful for this ?
Thanks, Deepti
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kashyap_path10 •
1 answer
-Yes, those should be RSEM expression values.The expression values could be 0 for genes.
-cBio portal has z-scores as well,(which could be in negative).
-Expression values can be converted to log scale for heat maps/visualizations.
-For doing differential expression analysis,you can follow these tutorials:
Dear Tris,
As mentioned above I have downloaded the TCGA data from cBioPortal. I would like to know about ‘data_RNA_Seq_v2_expression_median’. This have values like following:
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
To do differential expression analysis "Ron" mentioned some tutorials but those are with raw counts data. I would like to know how to do differential analysis with the above mentioned table. Do I need to transform the data before using for Differential analysis? Could you please tell something about this?
Thank you
Hello, Thank you for the replies.
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