cohort: NanoString Experiment Cohorts

In nanostringr: Performs Quality Control, Data Normalization, and Batch Effect Correction for 'NanoString nCounter' Data

NanoString Experiment Cohorts

Description

There were five different cohorts used in NanoString experiments.

Usage

hld.r

ovd.r

ovc.r

hlo.r

ovo.r

Format

• hld.r Hodgkin Lymphoma Clinical Samples: a data frame with 232 rows and 77 columns

• ovd.r Ovarian Cancer Clinical Samples: a data frame with 133 rows and 261 columns

• ovc.r Ovarian Cancer Cell Lines: a data frame with 133 rows and 29 columns

• hlo.r DNA Oligonucleotides for the HL CodeSet: a data frame with 40 rows and 71 columns

• ovo.r DNA Oligonucleotides for the OC CodeSet: a data frame with 133 rows and 138 columns

An object of class data.frame with 232 rows and 77 columns.

An object of class data.frame with 133 rows and 261 columns.

An object of class data.frame with 133 rows and 29 columns.

An object of class data.frame with 40 rows and 71 columns.

An object of class data.frame with 133 rows and 138 columns.

Details

Each data object contains raw expression counts, so no normalization has been applied. The format is a data frame with genes as rows, samples as columns. Note that the first three columns contain gene metadata and are always labelled "Code.Class", "Name", and "Accession", and the rest are sample names. Hence, for the hld.r data, the raw counts are contained in 232 genes for 77 - 3 = 74 samples. The total number of samples is 74 + 258 + 26 + 68 + 135 = 561, which matches the number of rows in expQC, the expression QC data.

Source

See Table 1 of https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0153844 for details.

See Also

expQC

nanostringr documentation built on June 22, 2024, 10:17 a.m.