Entering edit mode
4.8 years ago
shweta.johari13
▴
30
Good evening Peeps! I have done ssGSEA using R studio as well as Gene Pattern. However, whenever I try to make a heatmap from the output from R which is the combined.gct, pvalues.gct, scores.gct, the heatmap is not generated on GenePattern but an error is shown. Nonetheless, when I do ssGSEA using Gene Pattern and use that output in Gene Pattern for Heat Map generation, it happens. Does anyone know why is this happening? If the output is made by R, I cant create any heatmap elsewhere but R? Any suggestions, please do let me know!!
Truly thanking you.
Please include some code snippets and the errors produced. A
head()of whatever data object is being fed into each program would also be helpful. Without any of this, answering your question is near impossible. As to your second part, popular options for making heatmaps from data.frame's in R are ComplexHeatmap and pheatmap.An error occured while reading the file final_ssGSEA-scores.gct. Cause: Unknown version on line 1.
I understand that when I perform ssGSEA using R, the output is different than in Gene Pattern even though the files are in .gct format. Thereby, I need to know how the files differ and how I can use the R output of ssGSEA to make a representation and thank you so much, I shall look into the heat maps thank you.