hi, I currently downloaded the data_RNA_Seq_v2_expression_median.txt from cbioportal. I found the read_counts is not integer and I don't know how to process this type of normalized data with Deseq2.
Should I download the previous-leveled data from portal and use Deseq2 from bottom to the top, or is there other package to find out the differentially expressed genes?
Hugo_Symbol TCGA-BJ-A0YZ-01 TCGA-BJ-A0Z0-01 TCGA-BJ-A0Z2-01
UBE2Q2P2 1.8867 2.6927 10.0867
HMGB1P1 139.6335 181.2141 203.7297
LOC155060 45.3978 131.8725 248.4856
RNU12-2P 0.4165 0.3948 0.9502
SSX9 0 0 0
CXORF67 0 1.1845 2.3756
Hope some with experience handling the pre-processed data from TCGA could answer this question.
Many thanks!
Michael
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zhangyunjie1992 •
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Edit: 14th May, 2020:
better to obtain the HT-seq raw counts from Xena Browser and process those in DESeq, following this guidance: A: Normalisation of RNAseq data from UCSC Xena Browser
Original answer:
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For DESeq2, you should obtain the raw counts. This data from cBioPortal is already normalised.
However, if you obtain the Z-scores from cBioPortal, then, according to cBioPortal, you can infer that something is higher in tumour if it has a Z-score >=2.
If you want the raw counts, you can obtain those from the GDC Data Portal.
Kevin
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