HCC study quality-control injections

Usage

glyhub_PXD065283_N_QC(
  kind = c("curated", "raw"),
  cache_dir = getOption("glyhub.cache_dir", tools::R_user_dir("glyhub", "cache")),
  refresh = FALSE,
  offline = FALSE
)

Source

https://doi.org/10.1002/advs.202516299.

Arguments

kind: "curated" returns a data object; "raw" returns the path to a verified source archive. Raw archives are currently available for CPTAC.
cache_dir: Cache directory, defaulting to tools::R_user_dir("glyhub", "cache"). Set option glyhub.cache_dir to change the default.
refresh: Download the pinned resource again, even if cached.
offline: Prohibit downloads; require a verified local resource.

Value

A glyexp::GlycoproteomicSE.

Details

8,030 source feature rows across 30 reported measurement columns.

Assay scale: Source linear MBR-derived glycosite/glycan quantities; upstream normalization not independently established

Source selection: Linear QC matrix chosen; clinical DE-selected log2 table is a separate cohort dataset.

All source cells preserved; no new normalization, imputation, filtering, inverse transform or aggregation

Source reports match-between-run quantification; source blank values retained as NA

30 QC injections (13 days, 3 repeated injections, 14 batch QC runs), not 30 independent people

No exponentiation to claim recovered original intensity; unspecified upstream settings remain unknown

Measurement columns are not automatically independent biological samples. Source row identifiers, annotations and provenance are retained in metadata.

The assay preserves source numeric values. The metadata field raw_abundance means source numbers; it does not certify that the authors supplied unprocessed intensity.

Availability and source license

Downloaded from the existing data release through the verified cache. Source-license scope for the complete object remains unresolved; no new license is granted. See publication-decisions.tsv and object metadata for original sources and limitations.