P-GSE32376-1 - P-GSE32376-1

Type
normalization data transformation protocol
Description
From raw data, gBG Sub Signal from four control and treated samples was taken for further analysis. Then median of all signals was taken and this was used as an input file for normalization by using R method. After normalization by R method, we obtained output file in which we applied Z-score statistical test. Given below is the algorithm used to generate normalized data provided in the VALUE column. Algorithm used in R for data normalization Step1: x<- read.table("input_file.txt",header=T,row.names=1,sep="\t") Step 2: log_x<-log(x,base=2) Step3: attach(log_x ) Step4: cnt<-(1/8)*(sort(Signal_1)+sort(Signal_2)+sort(Signal_3)+sort(Signal_4)+ sort(Signal_5)+sort(Signal_6)++sort(Signal_7)+sort(Signal_8)) Step5: value_1<-c(rank(Signal_1)) Step6: value_2<-c(rank(Signal_2)) Step7: value_3<-c(rank(Signal_3)) Step8: value_4<-c(rank(Signal_4)) Step9: value_5<-c(rank(Signal_5)) Step10: value_6<-c(rank(Signal_6)) Step11: value_7<-c(rank(Signal_7)) Step12: value_8<-c(rank(Signal_8)) Step13: final<-cbind(value_1,value_2,value_3,value_4,value_5,value_6,value_7,val ue_8) boxplot(final) Step14: write.table(final,"f//priyanka/R method/result.txt") Step15: write.table(final,"result.txt") ID_REF = VALUE = Normalized signal intensity
Links
Experiment E-GEOD-32376