Autism cell-line example data set

Description

Example data set for analysing phenotype microarray data that were not recorded with an OmniLog(R) instrument.

Format

boccuto_et_al is a MOPMX object with four OPMX objects of the dimension 35 x 1 x 96 as elements. The plate types are ‘CUSTOM:PM-M01’ to ‘CUSTOM:PM-M04’. The well assignment of these is fully identical to their non-custom counterparts, but separate plate types are nevertheless useful here to avoid comparing apples and oranges, as the scale of the measurements is totally different from OmniLog units.

Details

The data set is identical to the supplement of Boccuto et al. (2013) except for the following differences:

• The measurements are the original, not yet log-transformed ones.

• The negative controls are contained, hence the plates are complete.

• The individuals N1 to N15 are missing, hence the data set is reduced to autism-spectrum disorder patients and control group.

The data are point measurements, so a call to do_aggr would just copy the data. Two of the metadata entries are important, ‘individual’ for identifying the cell culture and ‘group’ for assigning the individuals to patients and control group, respectively.

Note

Information provided by C.E. Schwartz and colleagues additional to the supplement of Boccuto et al. (2013) is gratefully acknowledged.

References

Boccuto, L., Chen, C.-F., Pittman, A.R., Skinner, C.D., McCartney, H.J., Jones, K., Bochner, B.R., Stevenson, R.E., Schwartz, C.E. 2013. Decreased tryptophan metabolim in patients with autism spectrum disorder. Molecular Autism 4: 16.

Schwartz, C.E., pers. comm.

Examples

# This yields a variable 'boccuto_et_al' containing the data.
data(boccuto_et_al)

# Pseudo-aggregate the data (use a copy of each point measurement as
# maximum-height value).
boccuto_et_al <- do_aggr(boccuto_et_al)

# Copy the well maps of the pre-defined counterparts.
register_plate(`CUSTOM:PM-M01` = wells(plate = "PM-M01"))

## CUSTOM:PM-M01 
##          TRUE

register_plate(`CUSTOM:PM-M02` = wells(plate = "PM-M02"))

## CUSTOM:PM-M02 
##          TRUE

register_plate(`CUSTOM:PM-M03` = wells(plate = "PM-M03"))

## CUSTOM:PM-M03 
##          TRUE

register_plate(`CUSTOM:PM-M04` = wells(plate = "PM-M04"))

## CUSTOM:PM-M04 
##          TRUE

# Now the data are ready for analysis.