Result only having Obsevation plot and not Reference plot

[Cristinacondel1]

Hi,

I have run successfully inferCNV on my data but the output image infercnv.png is only showing the observation heat map and not the reference ("normal") heat map. My division of cells consists only on Normal and Tumor groups. I was wondering what could be the reason for this.

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[GeorgescuC]

Hi @Cristinacondel1 ,

When you run the CreateInfercnvObject method, you provide as inputs:

• an annotations_file where the Tumor/Normal classification assignments of your cells should be (but it can also be individual cell types or any other classification information you have).
• a ref_group_names which defines which subset of cells are to be used as references based on the names in the annotations file. If your annotations file lists them as "Normal" or "Tumor", the value for this option should be c("Normal").

If no annotation is provided as ref_group_names, all cells are considered observations and the average of the whole dataset is used as baseline expression. There will be no reference plot in that case. Based on the figure's legend however, it seems like there are no cells defined as "Normal" in the annotations file. Is that the case?

Regards, Christophe.