[BioC] DART

[Lawler, Katherine]

Hi Martin,

Thanks again for the report and example file. To summarise our findings for the mailing list:

>>I have a table with expression values for 2000 genes, for 16 samples, rownames are EntrezGeneIDs and a vector which contains the signature, +1 or -1 for 200 genes, names are EntrezGeneIDs.
>> So I wanted to get the activity scores, but they are always "NA"  using
>>pred.o<-PredActScore(prNet.o$pradjMC,prNet.o$signMC,data)
>>[...]
>>So my question is: where did I a mistake, maybe my data has not the right format

The input expression data needs to be a matrix (for example using as.matrix(); see vignette or ?DoDART). 

>>Failure in if (netconsist > netconsist.v[4]) { :
>> Missing value, where TRUE / FALSE needed

This error comes from EvalConsNet() when the adjacency matrix (BuildRN()$adj) consists only of zeros.
DART could have a more helpful error message or a warning at that point. 
In the meantime, can I suggest performing a check after building the relevance network:

## Build the relevance network:
# rn.o <- BuildRN(..)

## How many edges in the relevance network? Look at the adjacency matrix.
numEdges <- sum(rn.o$adj == 1)/2
## Only continue if numEdges is > 0 :
# if(numEdges > 0){ .. continue.. }


best wishes,
Katherine

>________________________________________
>From: Lawler, Katherine
>Sent: 28 February 2014 22:50
>To: bioconductor at r-project.org; manrap91 at web.de
>Subject: RE: DART
>
>Dear Martin,
>
>Thanks for your questions, but I can't reproduce this from the descriptions.
>
>Could you provide a small reproducible example (for cut-and-paste) and the complete sessionInfo() output?
>
>It may be that the input data are not in the expected format or types; see the vignette or ?DoDART, and have a look at the example dataset:
>> data(dataDART)
>> head(dataDART$data)
>> head(dataDART$sign)
>
>best wishes,
>Katherine
>>________________________________________
>>From: Martin Garbe [guest] [guest at bioconductor.org]
>>Sent: 28 February 2014 18:05
>>To: bioconductor at r-project.org; manrap91 at web.de
>>Cc: Lawler, Katherine
>>Subject: DART
>>
>> I wanted to use DART (Denoising Algorithm based on Relevance network Topology).
>>I have a table with expression values for 2000 genes, for 16 samples, rownames are EntrezGeneIDs and a vector which contains the signature, +1 or -1 for 200 genes, names are EntrezGeneIDs.
>> So I wanted to get the activity scores, but they are always "NA"  using
>>pred.o<-PredActScore(prNet.o$pradjMC,prNet.o$signMC,data)
>>and there are warnings():
>>50: mean(<data.frame>) is deprecated.
>>Use colMeans() or sapply(*, mean) instead.
>>
>>So my question is: where did I a mistake, maybe my data has not the right format, but I get  normal results by using: print(evalNet.o$netcons)
>>
>>And the next problem is, that the program only runs, if the first column of my expression data is that one with the EntrezGeneID, deleting that column resulting in the failure:
>>Failure in if (netconsist > netconsist.v[4]) { :
>>Missing value, where TRUE / FALSE needed
>>
>> -- output of sessionInfo():
>>
>>R version 3.0.2 (2013-09-25)
>>Platform: x86_64-w64-mingw32/x64 (64-bit)
>>
>>locale:
>>[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
>>[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
>>[5] LC_TIME=German_Germany.1252
>>
>>attached base packages:
>>[1] stats     graphics  grDevices utils     datasets  methods   base
>>
>>
>>
>>--
>>Sent via the guest posting facility at bioconductor.org.
>>