Closed jharenza closed 1 year ago
@HuangXiaoyan0106 for your next weekly QC, can you grab the v11 histologies-base.tsv
for the file against which you will compare? Thanks!
@HuangXiaoyan0106 for your next weekly QC, can you grab the v11
histologies-base.tsv
for the file against which you will compare? Thanks!
@jharenza Weekly QC has been done, but I ran the script manually with v11 histologies-base.tsv
, and the results have been uploaded.
Thank you for your patience @HuangXiaoyan0106 !
A few notes on the combined_changes
file :
OS_days
? You will have to convert to numeric coming out of the WH since the WH cannot retain these as numeric without creating NULL fields in place of NA. Many of the OS_days are matching but come through in the report as not matching, presumably because one is numeric and one is character.age_last_update_days
, OS_status
, pathology_diagnosis
, pathology_free_text_diagnosis
, primary_site
, seq_center
, tumor_descriptor
can you only print those samples which have a difference between last and previous? OS_status
which went from DECEASED
to LIVING
! @youngnm can you take a look at these please?
BS_0YBAGHZ1
BS_3P9BQCDK
BS_C7FRTK6P
BS_DWRM8B7J
BS_BETQ48X0
BS_CK0BY1MB
BS_SZ9SVSBH
sample_id
? The leading zeroes are missing, but last week, they were fine in a file directly downloaded from the WH? Could it be a conversion issue?Tumor
to Not Reported
sample_type:
BS_BETQ48X0
BS_CK0BY1MB
BS_SZ9SVSBH
@HuangXiaoyan0106 can you also put the histologies-base-adapt.tsv
file which was used for each QC into the S3 bucket please (only starting with this latest one)?
@ewafula check to see if you also have access to this s3 bucket - v12 base histology file
Create meeting for Nick/Eric/JoLynne/Asif/AdamK to review histologies and d3b warehouse.
looking to streamline the histology workflows. Decision to put in PRs directly in the histology repository. Will modify the GTEx file to modify subgroups, and remove that code from downstream modules. Creating tables for mapping broad, short histologies to path dx, within the d3b wareshouse. (TBD- who maintains this - to discuss in the next toolkit meeting).
What data file(s) does this issue pertain to?
histologies.tsv
Put your question or report your issue here.
Implement https://github.com/d3b-center/D3b-codes/tree/master/weekly_qc (https://github.com/d3b-center/D3b-codes/blob/master/weekly_qc/01-QC_histology.Rmd) for
histologies-base.tsv
Who will do this?
@HuangXiaoyan0106 @yuankunzhu
cc @aadamk