Description Format Details Note References Examples
Example data set for analysing phenotype microarray data that were not recorded with an OmniLog(R) instrument.
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.
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.
Information provided by C.E. Schwartz and colleagues additional to the supplement of Boccuto et al. (2013) is gratefully acknowledged.
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 | # 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"))
register_plate(`CUSTOM:PM-M02` = wells(plate = "PM-M02"))
register_plate(`CUSTOM:PM-M03` = wells(plate = "PM-M03"))
register_plate(`CUSTOM:PM-M04` = wells(plate = "PM-M04"))
# Now the data are ready for analysis.
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.