Question: How to handle data_RNA_Seq_v2_expression_median from TCGA
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gravatar for zhangyunjie1992
10 months ago by
zhangyunjie199220 wrote:

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

rna-seq tcga • 524 views
ADD COMMENTlink modified 11 days ago by Kevin Blighe21k • written 10 months ago by zhangyunjie199220
0
gravatar for Kevin Blighe
11 days ago by
Kevin Blighe21k
University College London Cancer Institute
Kevin Blighe21k wrote:

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

ADD COMMENTlink modified 11 days ago • written 11 days ago by Kevin Blighe21k
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