Calculating AUC for individual Probe ID(affy)

Question

[David_emir]

Hi All,

I am facing problem while calculating AUC using pROC package (R/Bioconductor) . My data consists of 21 samples (nrow) of which 13 disease and 8 control ~34500 Column of Probe_ID(affy_Ids).

My Goal is to calculate AUC of each Probe_Id(genes) using Disease V/s Column. i.e AUC fo individual genes.

I have processed the file and used the following code

install.packages("pROC")
library(pROC)
auc_ci_results <-sapply(3:ncol(res),function(i){roc(as.factor(res$X.Status.),as.numeric(res[,i]),auc=T,ci=T)})
write.table(auc_ci_results,file="auc_ci_only.txt",row.names=T, sep="\t")

Please Note: res is my matrix of 22 Rows and 34500 Cols It looks like:

Sample         Status     Probe_ID 1
"GSM333437"    Disease    -0.53953211
"GSM333436"    Control    -0.3076905
"GSM333450"    Disease    -0.41491226

(I have 34500 columns like this, each column is a Probe id)

When I executed the code above, I got the following output:

AUC     0.682692307692308      0.413461538461538      0.759615384615385      0.615384615384615       0.826923076923077       0.740384615384615
CI      c(0.44468236738601,    c(0.52852770916173,    c(0.44468236738601,    c(0.617953423075478,    c(0.617953423075478,    c(0.617953423075478,
        0.682692307692308,     0.759615384615385,     0.682692307692308,     0.826923076923077       0.826923076923077,      0.826923076923077,
        0.920702247998605)     0.990703060069039)     0.920702247998605)     1)                      1)                      1)

I got 7 AUC values.

Requirement: I need individual AUC values for each GENES.

Please help me out, I tried all possible ways to solve, but failed. Please let me know where I am going wrong.

Thanks a lot, your help means a lot to me,

Thanks in advance

-Ateeq