AUC for DIABLO object

Hello,

I am using DIABLO to integrate transcriptomics and proteomics in order to identify a signature made up of ~2 transcripts and ~2 genes.

I have identified the signature using block.splsda, and now I would like to use leave one out cross validation to find out the AUC of the combined signature (genes and proteins).

I have used the perf function, however it will not provide the AUCs. This is the code I have ran:
perf.null <- perf(diablo.res.null, validation = ‘loo’, auc = TRUE,
nrepeat = 2, dist = ‘mahalanobis.dist’)

When I do perf.null$auc, auc is empty.
Is there an alternative way to do cross validation and then obtaining the combined cross-validated AUC?

Many thanks in advance,
Heather Jackson

Hi Heather,
Once you have your parameters keepX etc, run a full block.splsda on the whole data set and then:
auroc(object).

However, we won’t perform cross validation in this case, so we will follow up on this perf() code in the meantime.
Note: if you do leave-one-out cross-validation, you do not need to repeat the CV, only onces covers all possibilities!

Kim-Anh

Hi Kim-Anh,

Thanks a lot for your reply, and for pointing out about leave-one-out cross validation!

So is it only possible to see the AUC for each block individually, rather than the combined AUC?

Thanks
Heather