From: Keizer_71 <christophe.lo_at_gmail.com>

Date: Tue, 04 Mar 2008 00:56:54 -0800 (PST)

*#############filter out low variance and Select 10,000
*

probesets##############

Date: Tue, 04 Mar 2008 00:56:54 -0800 (PST)

Hi Everyone,

Thanks for all the help with the previous queries.

Here is what i want to do. i have 20000 probesets-->calculate all the variance accross all the probesets-->filter out probesets that are low so now i ended up with only 10000. The 10000 is fine but when i export to excel, it is missing the probeID. Here are my code and examples.

#########calculate the variance across the probesets and plot

signals#########

library(xlsReadWrite)

x<-1:20000

y<-2:141

data.matrix<-data.matrix(data[,y])#create data.matrix
variableprobe<-apply(data.matrix[x,],1,var)
variableprobe #output variance across probesets
hist(variableprobe) #displaying histogram of variableprobe
write.xls(cbind(data[1],

Variance=apply(data[,y],1,var)),file='c://variance.csv')

#export as a .csv file.

Output:

ProbeID Variance 224588_at 21.58257457

##############################################################################

probesets##############

data.sub = data.matrix[order(variableprobe,decreasing=TRUE),][1:10000,] dim(data.sub)

write.table(data.sub, file = "c://data_output.csv", sep = ",", col.names = NA)

Output:

Sample_1_D Sample_1_C Sample_2_D Sample_2_C 1 2.425509867 11.34031409 11.46868531 11.75741478

what i need is this

ProbeID Sample_1_D Sample_1_C Sample_2_D
Sample_2_C

1 224588_at 2.425509867 11.34031409 11.46868531
11.75741478

This is just the short version but there are 10000 rows and 140 columns.

thanks

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