**20**wrote:

First, I pre-process my dataset (TCGA breast cancer including GE and CNA) like the way the below paper did on TCGA cutaneous melanoma: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5559859/pdf/12864_2017_Article_3990.pdf (Data analysis, Page 9 of 12)

At the end of pre-processing, I have TCGA BRCA Gene expression (478 genes - 981 samples) and TCGA BRCA CNA (589 genes - 981 samples), assigned as *c_exp* and *c_cna* , respectively. For the above study, they process their dataset and then perform integrative analysis using the analysis tool **ANCut**.

Next, the above group of authors developed a novel tool: **AWNCut**: https://www.ncbi.nlm.nih.gov/pubmed/30094873 and continue to use the above pre-processed dataset (**ANCut**) to perform analyses using **AWNCut**.

Now, I've been applying my pre-processed dataset to AWNCut.

```
#library
source("AWNCut_fun.R") #https://github.com/shuanggema/AWNCut/blob/master/AWNCut_fun.R
#This sets up the initial parameters
lambda <- seq(1,15,0.5) #Tuning parameter lambda
Tau <- seq(0.1,1.5,0.1) #Tuning parameter tau
K=7; #Number of clusters
X=t(c_exp) #row=patients, column=gene
Z=t(c_cna) #row=patients, column=gene
Tune1 <- AWNcut.TuningSelection(X, Z, K, lambda, Tau, B=500, L=1000)
```

I run into a problem:

Error in if (OP.value <= OP.value.old) {:

Missing value where TRUE/FALSE needed

In addition: there were 50 or more warnings

I do some researches and know that I get this problem when I am trying to compare the missing value (NA, NAN,...) with boolen value (TRUE/FALSE). But when I check my dataset:

```
tableis.na(c_exp))
#FALSE
#468918
tableis.na(c_cna))
#FALSE
#577809
table(is.finite(c_exp))
#TRUE
#468918
table(is.finite(c_cna))
#TRUE
#577809
```

Please help me clarify what problem I am facing? Any suggestion is appreciated!

Have you ran

`debug(AWNcut)`

and caledl`AWNcut.TuningSelection`

with your input? From the source code https://github.com/shuanggema/AWNCut/blob/1af5af8498acfdddb69938bab9cbf58fe04de96c/AWNCut_fun.R there seems to be a few places where a missing value could arise5.5kHi Russhh, I've just written additionally a code line like you said: debug(AWNcut) and it doesn't report any problem?

And what does "caledl AWNcut.TuningSelection with your input" means? can you figure it out?

20Sorry, that was a typo. Call

`AWNcut.TuningSelection`

with your input ...5.5kThere's an introduction to using the debugger in "Advanced R": https://adv-r.hadley.nz/debugging.html#browser

5.5k20I assigned

c_expto X,c_cnato Z, K=7, lambda = seq(1,15,0.5), and Tau <- seq(0.1,1.5,0.1) as you can see, in whichc_expandc_cnaare my two data as matrix equivalent to gene expression and CNA, respectively20