The number of elements of the gene set is less than the minimum allowed.

[pgm99]

Dear Antonio, I'm using your fantastic tool for the analysis of a melanoma single cell datasets. Everything works just fine, except for a sample. Its the same cell line with different treatments, almost same gene set and more or less cells. This is the output and my error:

[1] " raw data - genes: 33694 cells: 4328"
[1] "1) Filter: cells > 200 genes"
[1] "low data quality"
[1] "2) Filter: genes > 5% of cells"
[1] "8656 genes past filtering"
[1] "3) Annotations gene coordinates"
The number of elements of the gene set is less than the minimum allowed.

Thanks in advance

[Serine94209792]

I also encountered the same problem,have you solved it?

[pgm99]

Unfortunately no. I'm still waiting for an answer while I try other samples (so far without the same problem, I don't really understand)

[Serine94209792]

Unfortunately no. I'm still waiting for an answer while I try other samples (so far without the same problem, I don't really understand)

Thanks, I will try other datesets later.

[AntonioDeFalco]

@pgm99 @Serine94209792

Thanks for the feedback, i will try to solve the problem. Are you analysing mouse or human samples?

[pgm99]

@AntonioDeFalco Thanks for the reply and the help. I'm analysing human samples (4 melanoma samples from the same BRAF-mutant cell line). The problem came only with one of them (GEO: GSM5022595).
Again, thanks in advance

[Serine94209792]

@AntonioDeFalco Hello, thanks for reply. I am using human colon cancer samples.

[pgm99]

@AntonioDeFalco Hi again, any advance in this issue? If you need any extra information or details I am at your complete disposal. Thanks again for your work

[pgm99]

Hi again. We finally found some kind of fix. As my sample is all tumor I needed to provided SCEVAN a vector with normal cells (even though I don´t have normal cells, I just selected 20-30 random tumor cells as normal). I did not get the full output (clone tree, tsne graphs and pathway graphs are missing). At least I got the subclones files.
If anybody found a better solution or need some details about this I will provide them