jyyulab / netbid Goto Github PK

The DA/DE P values show on the plot are different from the ones in the master table. There is a bug when converting Z-score to P value in the plot function.

I checked my data and there is no na/nan. However, it still report the error in draw.emb.kmeans ,as following:
Error in quantile.default(as.numeric(x), c(0.25, 0.75), na.rm = na.rm, :
missing values and NaN's not allowed if 'na.rm' is FALSE

Hi Sherry,

We need to update the get_IDtransfer() function to include an argument useCache = F within getBM() function from biomart. I have attached a working version of the modified function, can you please update the function and release it with new netbid2. Thanks!.

-Yogesh
get_IDtransfer.txt

In the rare cases when there is a driver which we have DA values for, but whose corresponding gene was not in the expression matrix (resulting in NA values in the DE columns), the draw.GSEA.NetBID() function glitches. It does not cause a visible error, but the plot will display incorrect DE p-values in the DE column. I assume this is due to the NA values being ignored, so the ordering of the DE genes/DA drivers gets thrown out of alignment.

Quitting from lines 75-91 (afterQC_filt0.5_PDX80QC.Rmd)
Error in apply(s1, 1, min) : dim(X) must have a positive length
In addition: Warning message:
In dir.create(outdir, recursive = TRUE) :

Error in apply(s1, 1, min) : dim(X) must have a positive length

draw.bubblePlot(driver_list= driver_list,show_label=ms_tab[driver_list,'gene_label'],
Z_val=ms_tab[driver_list,sprintf('Z.%s_DA',comp_name)],
driver_type=ms_tab[driver_list,'gene_biotype'],
target_list=analysis.par$merge.network$target_list,transfer2symbol2type=transfer_tab,
bg_list=ms_tab[,'geneSymbol'],min_gs_size=5,max_gs_size=500,use_gs="all",
top_geneset_number=15,top_driver_number=20,
pdf_file = sprintf('%s/bubblePlot2.pdf',analysis.par$out.dir.PLOT),
main='Bubbleplot for top driver targets')

“Error in xy.coords(x, y) : 'x' and 'y' lengths differ”

when I set up draw.bubblePlot>15, draw.bubblePlot will results in an error that show “Error in xy.coords(x, y) : 'x' and 'y' lengths differ”

Thank you for making such a great tool!
When I run the NetBID tutorial, I don't get error when I use the function getDE.BID.2G, but I get a lot of warnings. i haven't changed the tutorial code except for some paths. can you help me to find out why?