read_data: Read Seahorse Wave Excel File

In ceas: Cellular Energetics Analysis Software

Read Seahorse Wave Excel File

Description

Reads input seahore data from an excel Seahorse Wave File. It assumes your data is background normalized.

Usage

read_data(
  rep_list,
  norm = NULL,
  sheet = 2,
  delimiter = " ",
  norm_column = "exp_group",
  norm_method = "minimum"
)

Arguments

rep_list	A list of Seahorse Wave excel export files. One file per replicate. If your data is in a directory called "seahorse_data", use list.files("seahorse_data", pattern = "*.xlsx", full.names = TRUE) to make a list of the excel files. Add multiple replicates with care - see details.
norm	A csv file with the experimental groups and their normalization values. Leave unset if normalization is not required. See normalize().
sheet	The number of the excel sheet containing the long-form Seahorse data. Default is 2 because the long-form output from Seahorse Wave is on sheet 2
delimiter	The delimiter between the group name and the assay type in the Group column of the wave output. e.g. "Group1 MITO" would use a space character as delimiter.
norm_column	Whether to normalize by "Well" or "exp_group" column. The first column of the normalization csv provided should match this value.
norm_method	How to normalize each well or experimental group (specified by norm_column): by its corresponding row in the norm csv ("self") or by the minimum of the measure column in the provided norm csv ("minimum"). See the normalize() function for more details.

Details

Although ceas enables integration of multiple biological and/or technical replicates, previous work has reported high inter-plate variation (Yepez et. al 2018). If you don't want your replicate data combined, you can either:

• make sure that the names of the common groups between the replicates are different.

• in downstream analyses (get_energetics_summary, bioscope_plot, rate_plot, atp_plot), use sep_reps = TRUE to do all calculations and plotting separately for each replicate.

NOTE: to maintain backwards compatibility sep_reps is currently FALSE by default, but will be set to TRUE in a future release.

Value

a seahorse_rates table

References

Yépez et al. 2018 OCR-Stats: Robust estimation and statistical testing of mitochondrial respiration activities using Seahorse XF Analyzer PLOS ONE 2018;13:e0199938. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1371/journal.pone.0199938")}

Examples

rep_list <- system.file("extdata", package = "ceas") |>
  list.files(pattern = "*.xlsx", full.names = TRUE)
seahorse_rates <- read_data(rep_list, sheet = 2)
head(seahorse_rates, n = 10)

# normalization by well using raw cell count or protein quantity
norm_csv <- system.file("extdata", package = "ceas") |>
  list.files(pattern = "well_norm.csv", full.names = TRUE)
seahorse_rates.norm <- read_data(
  rep_list,
  norm = norm_csv,
  norm_column = "well",
  norm_method = "self",
  sheet = 2
)
head(seahorse_rates.norm, n = 10)

ceas documentation built on April 3, 2025, 8:34 p.m.