I am attempting to follow the Galaxy tutorial for reference-based RNA-sequencing (https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html#visualization-of-the-differentially-expressed-genes).
Using Galaxy, I have successfully (1) extracted the most DE genes from the normalized counts table and (2) extracted the normalized counts into a table. Currently, I am attempting to visualize my differential expressed genes. I have been unable to plot the heatmap with my normalized counts using the tool heatmap2. I could not find others in the community with a similar issue. Any help would be greatly appreciated!
I am using the tool heatmap2 (toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/2.2.1+galaxy1).
Parameters used were:
Data transformation - Log2(value) transform my data
Enable data clustering - True
Labeling columns and rows - Label columns and not rows
Coloring groups - Blue to white to red
Data scaling - Do not scale my data
Tool generated the following standard error:
Fatal error: Exit code 1 ()
Attaching package: ‘gplots’
The following object is masked from ‘package:stats’:
Error in hclust(x, method = “complete”) :
NA/NaN/Inf in foreign function call (arg 11)
Calls: heatmap.2 -> hclustfun -> hclust