createData {maanova} | R Documentation |
This is the function to create a madata
object based on the
given rawdata
and some parameters.
createData(rawdata, n.rep=1, avgreps=0, log.trans=TRUE)
rawdata |
An object of class rawdata , which should be the result
from read.madata . |
n.rep |
An integer to represent the number of replicates. |
avgreps |
An integer to indicate whether to average the replicates or not. 0 means no average; 1 means to take the mean of the replicates; 2 means to take the median of the replicates. |
log.trans |
A logical value to indicate whether to take log2
transformation on the raw data or not. It is TRUE by default. But
in the case that your data is pre-transformed, you need to set it to
FALSE. If this is TRUE, TransformMethod field will be set to
"log2". |
The data integrity is checked before making the object. The number of rows for the data must be consistent with the number of replicates; the number of columns for the data must be consistent with the number of dyes, etc.
Users have the option to collapse the replicated spots. Collapsing
will be done by taking mean or median of the intensity values for the
replicated spots. This function assumes the input data is on raw scale.
So if your data is pre-transformed and on a log2 based,
collapsing could be wrong. Also note that once
the replicated spots are collapsed, you will lose the grid location
and spatial loess ("rlowess" option in
transform.madata
will be unapplicable for it.
An object of class madata
, which is a list of following components:
n.gene |
Total number of genes in the experiment. |
n.rep |
Number of replicates in the experiment. |
n.spot |
Number of spots for each gene. |
data |
data field. It is either the log2 transformed rawdata (if log.trans=TRUE), or just the rawdata (if log.trans=FALSE). |
Others |
All other fields in the input object of class rawdata . |
Hao Wu hao@jax.org
################# # 2-dye arrays ################# data(paigen) # create data object with replicate data2 <- createData(paigen.raw, n.rep=2) # summarize the data object summary(data2) # create data with averaging of replicates data1 <- createData(paigen.raw, n.rep=2, avgreps=1) summary(data1) #################################################################### # affy array - data is pre-transformed so log2 is skipped #################################################################### data(abf1) abf1 <- createData(abf1.raw, n.rep=1, log.trans=FALSE) summary(abf1)