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)