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Lawler, Katherine
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@lawler-katherine-5918
Last seen 9.6 years ago
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.
>>