Hello Dr. Peder Wong,


I am trying to follow the steps you mentioned for exiqon data analysis and
would like to know that is the
object *Logratio  *is considered to be normalized data that can be used for
further analysis work??


rownames(RG) <- RG$genes[,6] #I use that to sum over spot replicates
RGb = backgroundCorrect(RG, method="normexp", offset=50)

cy3.channel = RGb$R
cy3.channel.norm =normalizeBetweenArrays(log2(cy3.channel),
method="quantile")
#this is the Logscaled Cy3 data with four spots per probe

cy5.channel = RGb$G
cy5.channel.norm =normalizeBetweenArrays(log2(cy5.channel),
method="quantile")
#this is the Logscaled Cy5 data with four spots per probe

MA = normalizeWithinArrays(RGb, method="loess", weights=RGb$weights)
log.ratio <- MA$M # this is the Ratio data with four spots per probe

#The median of the replicate probes:

Cy3.norm <-
apply(cy3.channel,2,function(v){tapply(v,names(v),function(x){median(x,n
a.rm=TRUE)})})

Cy5.norm <-
apply(cy5.channel,2,function(v){tapply(v,names(v),function(x){median(x,n
a.rm=TRUE)})})

*LogRatio <-
apply(logratio,2,function(v){tapply(v,names(v),function(x){median(x,na.r
m=TRUE)})})*
**
*Thanks*
*Ashwin *

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