Question: XHMM error: Error in heatmap.2(absCorrWithRemovedPC, Rowv = NA, Colv = NA, dendrogram = "none", :
0
gravatar for zhangqshxxzz
2.5 years ago by
zhangqshxxzz0 wrote:

bioinformatician

Hello ,everyone :

Can anyone have some suggests about this error, when I use XHMM draw the results in R..... `x' must be a numeric matrix

Thanks!

cnv xhmm R • 1.0k views
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by zhangqshxxzz0

What package/function did you use? (don't know what XHMM is...). How does your data looks like? What code did you use that lead to this error? Please provide as much information as possible, and ideally, a minimum reproducible example. Not clear this is a bioinformatics question.

ADD REPLYlink written 2.5 years ago by ddiez1.8k

(xhmm is a tool for finding structural variants in wes.) But OP should provide a lot more information here.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by WouterDeCoster40k
> XHMM_plots(PLOT_PATH,JOB_PREFICES,JOB_TARGETS_TO_GENES,SAMPLE_FEATURES)
Loading data from './DATA' XHMM run...
Read 2844 records
Read 7997 records
Reading 16 x 2844 named matrix
Reading 16 x 2420 named matrix
Read 0 records
Read 424 records
Reading 16 x 2420 named matrix
Reading 16 x 1 named matrix
Reading 16 x 16 named matrix
Read 1 record
Reading 16 x 2420 named matrix
Reading 16 x 2420 named matrix
Read 0 records
Read 0 records
Reading 16 x 2420 named matrix
Reading 16 x 2420 named matrix
Reading 16 x 2420 named matrix
Reading 16 x 2420 named matrix
Loading genes for dataset_1 targets
Error in heatmap.2(absCorrWithRemovedPC, Rowv = NA, Colv = NA, dendrogram = "none",  :
  `x' must be a numeric matrix

======================== I checked and compared the DATA files with other samples result, but the same step and parameter, it can run well in the other samples.....

ADD REPLYlink modified 2.5 years ago by WouterDeCoster40k • written 2.5 years ago by zhangqshxxzz0

I modified your post using the 101010 button for better readability. I also moved it to a comment, because it is no answer to your question.

ADD REPLYlink written 2.5 years ago by WouterDeCoster40k

Hello, maybe you have to load another library in R. library(gplots) library(plotrix) library(xhmmScripts) Try with these libraries loaded and maybe it will work. Regards Andrea

ADD REPLYlink written 5 months ago by andrea.citterio0
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