High-Throughput Screening example data - CMBA

Description

An example dataset containing High-Throughput Screening (HTS) output and experimental design information. See References for details.

Usage

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Format

A data frame with 80 rows and 9 columns:

  • Wells. Plate well numbers for each sample

  • Rows. Plate row identifiers for each sample

  • Columns. Plate column identifiers for each sample

  • S1_R1. Screen 1 Replicate 1

  • S1_R2. Screen 1 Replicate 2

  • S1_R3. Screen 1 Replicate 3

  • S2_R1. Screen 2 Replicate 1

  • S2_R2. Screen 2 Replicate 2

  • S2_R3. Screen 2 Replicate 3

This example data matrix consists of 6 plates with 80 wells each. Although these are 96-well plates, only 80 wells in each plate contained the active compounds. Therefore, the subsequent data matrix for this package excludes the inactive wells.

Details

The sights data format requires each plate matrix to be converted into a 1-dimensional vector. The plate wells in this vector should be arranged by row first. For example, this 3x3 plate matrix:

Col 1 Col 2 Col 3
Row A A1 A2 A3
Row B B1 B2 B3
Row C C1 C2 C3

can be converted into its vector form as:

Row Col Data
A 1 A1
A 2 A2
A 3 A3
B 1 B1
B 2 B2
B 3 B3
C 1 C1
C 2 C2
C 3 C3

Here, number of columns in a plate is 3, and number of rows is 3 as well. Each such plate vector should form a column in the data matrix before application of sights functions. Only the active wells should be included in the data matrix; inactive wells containing mock/control compounds should be marked as NAs, or if they are in entire rows/columns they can be removed completely as in this example dataset and the arguments plateRows and plateCols modified accordingly.

Value

Dataframe of 80 rows and 9 columns as explained in Format

References

CMBA Titration series 10uM Tyr samples. Murie et al. (2015). Improving detection of rare biological events in high-throughput screens. Journal of Biomolecular Screening, 20(2), 230-241.

Examples

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## load dataset
data(ex_dataMatrix)

## structure of dataset
str(ex_dataMatrix)
## summary of dataset
summary(ex_dataMatrix)

## See help pages of SIGHTS functions for examples of using this dataset