| selSpots {maigesPack} | R Documentation |
Function to select spots to be used in microarray normalisation.
selSpots(obj=NULL, sigNoise=1, rmFlag=NULL, gLabelsID=c("Name"),
remove=list(c("BLANK","DAP","LYS","PHE","Q_GENE","THR","TRP")),
badSpots=NULL, badLabel=NULL)
obj |
object of class maigesRaw. |
sigNoise |
positive real number indicating the cutoff to remove spots with signal-to-noise ratio below it. |
rmFlag |
vector of flag symbols to be removed (for
normalisation). These flags are stored in the slot Flags from
maigesRaw class. |
gLabelsID |
character vector indicating the gene labels to be
searched to exclude that ones specified in remove argument. |
remove |
list of same length as GlabelsID containing character
vector indicating the symbols of spots to be removed, according to
the GlabelsID argument. |
badSpots |
index of bad spots (numeric or logical) identifying
bad spots. May be the gene labels, with label ID specified by the
argument badLabel. |
badLabel |
character string specifying the gene label ID for
remove badSpots. |
This function takes the object of class maigesRaw and
actualise the slot UseSpots according with the arguments passed
to the function. This slot is read by the normalisation functions
normLoc, normOLIN,
normRepLoess, normScaleLimma and
normScaleMarray to use only the spots that passed the
criteria specified here.
This function returns another object of class maigesRaw
with the UseSpots slot actualised.
Gustavo H. Esteves <gesteves@vision.ime.usp.br>
## Loading the dataset
data(gastro)
## Filtering all spots with signal2noise ratio (Sf/Sb or Rf/Rb) greater
## or equal to 1 and that have 'Name' label as 'BLANK', 'DAP', ..., 'TRP'.
gastro.raw2 = selSpots(gastro.raw, sigNoise=1, rmFlag=NULL, gLabelsID="Name",
remove=list(c("BLANK","DAP","LYS","PHE","Q_GENE","THR","TRP")))
## To see the number of spots that suvived the filtering above do
apply(gastro.raw2@UseSpots, 2, sum)
## To do the same filtering as above, also filtering flags marcke as 1
## and 4 do
gastro.raw2 = selSpots(gastro.raw, sigNoise=1, rmFlag=c(1,4), gLabelsID="Name",
remove=list(c("BLANK","DAP","LYS","PHE","Q_GENE","THR","TRP")))
apply(gastro.raw2@UseSpots, 2, sum)