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Currently the assay_sample_info_tbl holds "libsize" and "normfactor" columns which make sense for RNA-seq-like count data, however we can't store other types of assay information on the sample level anywhere.
One way to fix this is to make a new assay_sample_covariate EAV table where we can add arbitrary covariates to the samples, like the sample_covariate table.
Once we do this, we'd remove the "libsize" and "normfactor" columns from assay_sample_info_tbl and put them as long covariates in the assay_sample_covariate table.
We would then remove the fetch_sample_statistics faciledata API function.
Create the assay_sample_covariate EAV table in the faciledata sql schema
Move libsize and normfactor for dataset,sample_id,assay_name combinations into that table
drop "libsize" and "normfactor" from assay_sample_info_tbl
remove fetch_sample_statistics from FacileData API
The text was updated successfully, but these errors were encountered:
lianos
changed the title
Create an assay_sample_covariate EAV db table
Add full support for (fetch|with)_assay_covariates to FacileData API
Apr 24, 2019
Currently the
assay_sample_info_tbl
holds"libsize"
and"normfactor"
columns which make sense for RNA-seq-like count data, however we can't store other types of assay information on the sample level anywhere.One way to fix this is to make a new
assay_sample_covariate
EAV table where we can add arbitrary covariates to the samples, like thesample_covariate
table.Once we do this, we'd remove the
"libsize"
and"normfactor"
columns fromassay_sample_info_tbl
and put them as long covariates in theassay_sample_covariate
table.We would then remove the
fetch_sample_statistics
faciledata API function."libsize"
and"normfactor"
fromassay_sample_info_tbl
fetch_sample_statistics
from FacileData APIThe text was updated successfully, but these errors were encountered: