MAE object missing gene expression data

[varsha090597]

Hi,

I am trying to use the cBioDataPack function within the package to pull the gene expression data for the Metastatic Prostate Adenocarcinoma (SU2C/PCF Dream Team, PNAS 2019) study (studyId: prad_su2c_2019). I am unfortunately only able to see the cna and mutation information in the MAE object. I have attached a screenshot of the command I tried running and the output I get. Any suggestions on this would be very helpful.

Thanks, Varsha

[LiNk-NY]

Hi Varsha,

This is what I see from the downloaded tarball. It doesn't look like there is any expression data in the file. All the other data should be in the metadata.

> downloadStudy("prad_su2c_2019")
Study file in cache: prad_su2c_2019
                                                                  BFC145 
"/home/user/.cache/R/cBioPortalData/21c324c7a529_prad_su2c_2019.tar.gz" 
> (ut <- untarStudy("/home/user/.cache/R/cBioPortalData/21c324c7a529_prad_su2c_2019.tar.gz"))
[1] "/tmp/RtmpmuZMlI/21c324c7a529_prad_su2c_2019"
> dir(file.path(ut, "prad_su2c_2019/"))
 [1] "data_clinical_patient.txt"                                 
 [2] "data_clinical_sample.txt"                                  
 [3] "data_cna_hg19.seg"                                         
 [4] "data_cna.txt"                                              
 [5] "data_fusions.txt"                                          
 [6] "data_mrna_seq_fpkm_capture_zscores_ref_all_samples.txt"    
 [7] "data_mrna_seq_fpkm_capture_zscores_ref_diploid_samples.txt"
 [8] "data_mrna_seq_fpkm_capture.txt"                            
 [9] "data_mrna_seq_fpkm_polya_zscores_ref_all_samples.txt"      
[10] "data_mrna_seq_fpkm_polya_zscores_ref_diploid_samples.txt"  
[11] "data_mrna_seq_fpkm_polya.txt"                              
[12] "data_mutations.txt"                                        
[13] "LICENSE"                                                   
[14] "meta_study.txt"

Perhaps this question is better suited for the cBioPortal Data team? https://github.com/cBioPortal/datahub

Best regards, Marcel

[varsha090597]

I think my issue was with the cbiodatapack function. The other assays that are listed here aren't accessible with the cbiodatapack function. The MAE I see has only 2 assays.

[LiNk-NY]

Hi Varsha, Please check the metadata:

metadata(prof)

[varsha090597]

Thanks. That answered my question.