Error in the vignette

[fcg-bio]

Hi,

I was running the vignette example, and after running the line > data_obj = featureConstruct(data_obj, method = "GlobalPanel");

I got the following error: Error in data[temp5, , drop = FALSE] : incorrect number of dimensions

[GIS-SP-Group]

Dear fcg-bio,

Would you please provide your full script starting from importing libraries and data set?

Huipeng

[fcg-bio]

Hi Huipeng,

Thanks for your quick response. I am running the commands as they are described in the vignette. My full script below

library(WGCNA)
library(flashClust)
library(gplots) 
library(preprocessCore) 
library(RCA)

### setting options 
options(stringsAsFactors = FALSE)

data_cellline = read.csv("data/GSE81861_Cell_Line_FPKM.csv",row.names=1)

fpkm_data = data_cellline;
color_to_use0 = colnames(fpkm_data);
color_to_use0 <- strsplit(color_to_use0,"__");
color_to_use <- paste("",lapply(color_to_use0,"[[",3),sep=""); color_to_use=gsub("\\.","#",color_to_use);

### construct data object
data_obj = dataConstruct(fpkm_data);
### filt out lowly expressed genes
data_obj = geneFilt(obj_in = data_obj);
### normalize gene expression data (Note: default is no normalization). data_obj = cellNormalize(data_obj);
### log transform the data
data_obj = dataTransform(data_obj,"log10");
### project the expression data into Reference Component space
data_obj = featureConstruct(data_obj, method = "GlobalPanel");
### generate cell clusters
data_obj = cellClust(data_obj);

On of the differences is that I am loading WGCNA 1.51, instead of 1.34

My Session Info

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RCA_1.0               preprocessCore_1.36.0 gplots_3.0.1          flashClust_1.01-2     WGCNA_1.51           
[6] fastcluster_1.1.22    dynamicTreeCut_1.63-1

loaded via a namespace (and not attached):
  [1] nlme_3.1-128         bitops_1.0-6         matrixStats_0.51.0   gmodels_2.16.2       doParallel_1.0.10   
  [6] RColorBrewer_1.1-2   prabclus_2.2-6       tools_3.3.1          backports_1.0.5      rgdal_1.2-5         
 [11] R6_2.2.0             rpart_4.1-10         KernSmooth_2.23-15   rgeos_0.3-22         Hmisc_4.0-2         
 [16] DBI_0.5-1            lazyeval_0.2.0       BiocGenerics_0.20.0  colorspace_1.3-2     trimcluster_0.1-2   
 [21] nnet_7.3-12          raster_2.5-8         sp_1.2-4             gridExtra_2.2.1      curl_2.3            
 [26] Biobase_2.34.0       htmlTable_1.9        expm_0.999-1         rmapshaper_0.2.0     diptest_0.75-7      
 [31] caTools_1.17.1       scales_0.4.1         checkmate_1.8.2      DEoptimR_1.0-8       classInt_0.1-23     
 [36] mvtnorm_1.0-5        robustbase_0.92-7    stringr_1.1.0        digest_0.6.12        foreign_0.8-67      
 [41] base64enc_0.1-3      dichromat_2.0-0      htmltools_0.3.5      limma_3.30.11        jsonvalidate_1.0.0  
 [46] htmlwidgets_0.8      RSQLite_1.1-2        impute_1.48.0        jsonlite_1.2         mclust_5.2.2        
 [51] gtools_3.5.0         spdep_0.6-11         acepack_1.4.1        dendextend_1.4.0     dplyr_0.5.0         
 [56] RCurl_1.95-4.8       magrittr_1.5         modeltools_0.2-21    GO.db_3.4.0          Formula_1.2-1       
 [61] geosphere_1.5-5      Matrix_1.2-7.1       Rcpp_0.12.9          munsell_0.4.3        S4Vectors_0.12.1    
 [66] viridis_0.3.4        stringi_1.1.2        whisker_0.3-2        yaml_2.1.14          MASS_7.3-45         
 [71] flexmix_2.3-13       tmaptools_1.2        plyr_1.8.4           grid_3.3.1           parallel_3.3.1      
 [76] gdata_2.17.0         deldir_0.1-12        lattice_0.20-34      splines_3.3.1        pander_0.6.0        
 [81] knitr_1.15.1         boot_1.3-18          fpc_2.1-10           geojsonlint_0.2.0    codetools_0.2-15    
 [86] stats4_3.3.1         LearnBayes_2.15      osmar_1.1-7          XML_3.98-1.5         V8_1.2              
 [91] latticeExtra_0.6-28  data.table_1.10.0    foreach_1.4.3        gtable_0.2.0         kernlab_0.9-25      
 [96] assertthat_0.1       ggplot2_2.2.1        e1071_1.6-8          coda_0.19-1          class_7.3-14        
[101] survival_2.40-1      tibble_1.2           iterators_1.0.8      AnnotationDbi_1.36.2 memoise_1.0.0       
[106] IRanges_2.8.1        cluster_2.0.5       

[GIS-SP-Group]

Hi, fcg-bio

I believe it is because the following line:

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ "###" normalize gene expression data (Note: default is no normalization). data_obj = cellNormalize(data_obj); ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ in which the normalization step was not executed ..

Try delete "data_obj" and rerun the whole script, with "data_obj=cellNormalize(data_obj)" in a new line.

all the best Huipeng

[fcg-bio]

Thanks Huipeng, sorry for the stupid copy/paste mistake Best

[GIS-SP-Group]

You're welcome! Let me know if you encounter any other issues or inconvenience.

best Huipeng