cytotox: Exposure time-concentration-response cytotoxicity data

In jcduda/td2pLL: Fitting a time-dose two-parameter log-logistic model to time-dose-response data

Exposure time-concentration-response cytotoxicity data

Description

A dataset containing cytotoxicity viability assay data of 30 compounds where the exposure time expo and concentration dose were varied in the experiment. For each compound, there are between 214 and 276 measurements.
For each compound, there are measurements of 3 donors.
For each compound and donor, there are 3 different exposure times (1, 2, and 7).
For each compound, donor and exposure time, there are mostly 6 (240 cases), rarely 7 (27 cases) or 8 (3 cases) different concentrations in milli molar (mM).
For each compound, donor, exposure time and concentration, there are mostly 3 measurements. For the control (concentration=0) there are often 8 measurements.

Usage

cytotox

Format

A data frame with 7064 rows and 12 variables:

compound

compound name

donor

donor within compound, factor

expo

exposure time in days

dose

concentration in mM

resp

normalized response: resp = (raw_resp / mean_resp) * 100

sample_id

sample within compound, donor and exposure time

donor_name

donor name

control_mean

Arithmetic mean of raw control (dose=0) measurements raw_resp for a compound, donor and exposure time. Sometimes, there are two sets of conrol measurements for such a setting. See by_control.

raw_resp

Raw measurements in mM

by_control

If "0", there was just one set of control measurements for a compound, donor and exposure time combination, which leas to control_mean and was always used for the normalization in resp.
If "1", there are 2 sets of control measurements and the first one (control_1 in original excel files) is used for this observation for normalization.
If "2", there are 2 sets of control measurements and the second one (control_2 in original excel files) is used for this observation for normalization.

left_asymp

Left asymptote calculated in when as additional pre-processing step (refitting) is applied.

resp_refit

New normalizes responses when as aditional pre-processing, refitting is applied. That means that for a given compound, donor and exposure time, a dose-response curve (4pLL) is fitted. The corresponding measurements are divided by the resulting left (upper) asymptote left_asymp and multiplied by 100. This way, the data is expected to better follow the assumption of a left asymptote of 100 percent.

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Source

https://doi.org/10.1007/s00204-018-2302-0

jcduda/td2pLL documentation built on May 14, 2022, 6:48 p.m.