Examine reference pool samples and apply normalization of study samples to their corresponding reference pool sample
normalize_isobaric(
omicsData,
exp_cname = NULL,
apply_norm = FALSE,
channel_cname = NULL,
refpool_channel = NULL,
refpool_cname = NULL,
refpool_notation = NULL
)an object of the class 'isobaricpepData'
character string specifying the name of the column
containing the experiment/plate information in f_data
logical, indicates whether normalization should be applied to omicsData$e_data
optional character string specifying the name of the
column containing the instrument channel a sample was run on in
f_data. This argument is optional. See Details for how to specify
information regarding reference pool samples. If using this argument, the
'refpool_channel' argument must also be specified; in this case,
'refpool_cname' and 'refpool_notation' should not be specified.
optional character string specifying which channel contains the reference pool sample. Only used when this is the same from experiment to experiment. This argument is optional. See Details for how to specify information regarding reference pool samples. If using this argument, the 'channel_cname' argument must also be specified; in this case, 'refpool_cname' and 'refpool_notation' should not be specified.
optional character string specifying the name of the
column containing information about which samples are reference samples in
f_data. This argument is optional. see Details for how to specify
information regarding reference pool samples. If using this argument, the
'refpool_notation' argument must also be specified; in this case,
'channel_cname' and 'refpool_channel' should not be specified.
optional character string specifying the value in the refpool_channel column which denotes that a sample is a reference sample. This argument is optional. See Details for how to specify information regarding reference pool samples. If using this argument, the 'refpool_cname' argument must also be specified; in this case, 'channel_cname' and 'refpool_channel' should not be specified.
If apply_norm = TRUE, an object of class 'isobaricpepData', normalized to reference pool, and with the attribute 'isobaric_info' updated to include information about the reference pool samples and the normalization procedure. Otherwise an object of class 'isobaricnormRes' containing similar information about the normalization process
There are two ways to specify the information needed for identifying reference samples which should be used for normalization:
specify channel_cname and refpool_channel. This should be
used when the reference sample for each experiment/plate was always located
in the same channel. Here channel_cname gives the column name for
the column in f_data which gives information about which channel
each sample was run on, and refpool_channel is a character string
specifying the value in channel_colname that corresponds to the
reference sample channel.
specify refpool_cname and
refpool_notation. This should be used when the reference sample is
not in a consistent channel across experiments/plates. Here,
refpool_cname gives the name of the column in f_data which
indicates whether a sample is a reference or not, and
refpool_notation is a character string giving the value used to
denote a reference sample in that column.
In both cases you must specify
exp_cname which gives the column name for the column in
f_data containing information about which experiment/plate a sample
was run on.
library(pmartRdata)
myiso <- edata_transform(isobaric_object, "log2")
# Don't apply the normalization quite yet;
# can use summary() and plot() to view reference pool samples
myiso_refpools <- normalize_isobaric(
omicsData = myiso, exp_cname = "Plex",
apply_norm = FALSE,
refpool_cname = "Virus",
refpool_notation = "Pool"
)
summary(myiso_refpools)
# Now apply the normalization;
# can use plot() to view the study samples after reference pool normalization
myiso_norm <- normalize_isobaric(
omicsData = myiso, exp_cname = "Plex",
apply_norm = TRUE,
refpool_cname = "Virus",
refpool_notation = "Pool"
)