Error in CreateInfercnvObject function

[Victor-K27]

Hi!

Thanks for making this package.

I have an issue with creating the infercnvobject, which I have been trying to troubleshoot unsuccessfully for some time now.

I am using the attached files as raw_counts_matrix, annotations_file, and gene_order_file (please have a look bellow).

infercnv_obj <- CreateInfercnvObject( raw_counts_matrix = "raw_counts_matrix_test.txt", annotations_file = "annotations_file_test.txt", gene_order_file = "gene_order_file_test.txt", delim = "\t", ref_group_names = c("nonTumor"), )

The error I am getting is:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 2 elements

I think it might have something to do with the formatting of my files, however, I have made it identical to that of the examples.

Thank you in advance for your precious time and help,

Sincerely, Victor

raw_counts_matrix_test.txt annotations_file_test.txt gene_order_file_test.txt

[GeorgescuC]

Hi @Victor-K27 ,

The annotation file you provided starts with the line "annotations_file[, 2]" which is not expected.

Regards, Christophe.

[Victor-K27]

Hi @GeorgescuC,

Thank you for your reply.

I have now fixed the annotations file (I think). Please find attached the new annotation, raw count matrix, and gene order file. I am getting a new error with these: Error in FUN(left, right) : non-numeric argument to binary operator

Any advice would be very helpful and extremely appreciated.

Thank you for your time, Best wishes,

Victor annotations_file_test_helen.txt gene_order_file_test.txt raw_counts_matrix_test_helen.txt

[Victor-K27]

I found the error, don't worry!

[Cristinex]

I found the error, don't worry!

I encountered the same error. How did you solve the problem?

[fangjialing]

@Victor-K27 , sorry, I have the same problem, can you tell me how did you solve the problem which is important for my project. thank you very much.