Entering edit mode
9.0 years ago
AHW
▴
90
During the use of codelink package to process raw codelink data, I got into some confusion when I look at the processed data. The processed data I got from GEO has four columns as below.
ID SignalIntensity SNR
1 109 7.5804349594 1.3421827372
2 110 11.2698560261 9.7509784076
3 111 8.6006358676 1.804853485
4 112 9.5435575539 3.2013768505
5 113 10.181235138 4.6459936834
6 114 8.1168949395 1.4226360984
7 116 8.4670495571 1.8682653573
8 117 8.2733657566 1.6663830675
9 118 5.4203308081 0.6769947295
10 119 8.5379673202 1.8326649796
11 120 9.7949416719 4.0503974531
12 121 5.9770829707 0.7442132887
13 123 5.7623248946 0.7208574513
14 124 5.3253576296 0.6793816015
15 125 8.3676877563 1.6437990197
Now I got raw data from GEO and tried to process it by codelink package with the following code
library(codelink)
codelink_processed <- list()
f = list.files(pattern = "TXT")
codelink_data <- function(data)
{
for(i in 1:length(f))
{
codset = readCodelinkSet(filename = f[[i]])
codset = codCorrect(codset, method = "half", offset = 0)
codset = codNormalize(codset, method = "loess", weights = getWeight(codset), loess.method = "fast")
exprs <- exprs(codset) ## to get SignalIntensity
snr <- getSNR(codset) ## to get SNR
dat <- cbind(exprs,snr)
codelink_processed[[length(codelink_processed)+1]] <- dat
print(head(codelink_processed[[1]]),10)
}
return(codelink_processed)
}
SignalIntensity SNR
1 7.197392657 0.7381305998
2 12.403618142 13.7535937689
3 8.749735373 1.7720060283
4 11.373505481 6.7607981511
5 11.348655741 6.5203397924
6 9.734132935 2.2048101666
I got the above data when I tried to process the raw data, however the second column is missing. Can any body tell me, where I am going wrong. Did I miss anything?