Dear All,
i started to read and use the tutorial for the BioNet package for the functional analysis of biological networks(http://www.bioconductor.org/packages/release/bioc/vignettes/BioNet/inst/doc/Tutorial.pdf), in order to implemented afterwards for finding interesting functional modules in my colon cancer microarray data analysis DE genes. More specifically, in page 15 of the vignette i used instead of the command ”heinz.py -e ALL edges 001.txt -n ALL nodes 001.txt -N True -E False” the runHeinz command :
runHeinz(heinz.folder="heinz_1.67", heinz.e.file="ALL_edges_001", heinz.n.file="ALL_nodes_001", N=TRUE, E=FALSE, diff=-1, n=1)
where heinz_1.67 is the name of the heinz folder, but i got the following warning:
Warning message:
running command 'cd heinz_1.67;heinz.py -e ALL_edges_001 -n ALL_nodes_001 -N True -E False -d -1 -s 1' had status 127
Afterwards the tutorial continued without error, but
datadir <- file.path(.path.package("BioNet"), "extdata")
Error: '.path.package' is defunct.
Use 'path.package' instead.
See help("Defunct")
And when i used datadir <- file.path(path.package("BioNet"), "extdata")
it didnt showed an error. These are some bugs with Bioconductor ? i have also downloaded CPLEX and installed it.
I am not the maintainer of BioNet (but I will alert them to this thread) but yes, .path.package() should not be used. I have updated it in release (version 1.26.1) and devel (version 1.27.1) so these will be available late tomorrow morning (Seattle time) via biocLite() and will clear up the error you're seeing (if you are using the release (3.0) or devel (3.1) versions of Bioconductor). I am not sure if this will clear up the other warning you saw, but hopefully the maintainer can speak to that.
i understand. Thus far, i didnt noticed a problem in the output, also in the file for the cytoscape--just some small number differences in the number of nodes-but i guess this is due to possible updates of limma and other packages. Moreover, i would like also to ask you one important question regarding the function nodeData in page 16:
nodeData(module, n = nodes(module), attr = "diff") <- fit2$coefficients[nodes(module), + 1]
Because i also implemented limma in my DE analysis prior to BioNet :
conditions <- data.imputed.eset$condition
condition <- factor(conditions, levels(condition)[c(2,1)])
pairs <- factor(rep(1:13, each = 2))
design <- model.matrix(~condition+pairs)
fit <- lmFit(data.imputed.eset, design)
fit2 <- eBayes(fit, trend=TRUE)
symbols <- unlist(mget(featureNames(data.imputed.eset), env=hgu133aSYMBOL))
top2 <- topTable(fit2, coef="conditionCancer", number=nrow(fit2), genelist=symbols, adjust.method="fdr", sort.by="none")
So, how i would transform the above function as in contrast with the vignette i have more than 1 coefficients and i want the fit2$coefficient= conditionCancer ?
Also i would like to ask one more important question regarding my dataset:
instead of importing the final image in cytoscape, i used the function:
plotModule(module, diff.expr = diff, scores = scores)--but the nodes arent coloured. Should i import the xgmml image in cytoscape ?