Open hannaeng opened 5 years ago
Hi Hanna,
Can you send me the output of str()
on your data frame? I suspect a column, maybe start or end is not numeric?
Hi Zachary,
Thank you for the clue! All my columns were factors…
Kind regards, Hanna
Hanna Engqvist, PhD student
hanna.engqvist@gu.se<mailto:hanna.engqvist@gu.se>
Sahlgrenska Academy at University of Gothenburg
Institute of Clinical Sciences
Department of Oncology
Tel: (+46) 31 7866751
Physical address:
Sahlgrenska Cancer Center
Medicinaregatan 1G, 6th floor
SE-413 90 Gothenburg, Sweden
Mailing address:
Sahlgrenska Cancer Center
University of Gothenburg
Box 425
SE-405 30 Gothenburg, Sweden
From: Zachary Skidmore [mailto:notifications@github.com]
Sent: Wednesday, May 29, 2019 5:17 PM
To: griffithlab/GenVisR <GenVisR@noreply.github.com>
Cc: Hanna Engqvist <hanna.engqvist@gu.se>; Author <author@noreply.github.com>
Subject: Re: [griffithlab/GenVisR] cnFreq did not detect identical genomic segments for all patients (#360)
Hi Hanna,
Can you send me the output of str() on your data frame? I suspect a column, maybe start or end is not numeric?
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Hi Hanna,
Can you send me the output of
str()
on your data frame? I suspect a column, maybe start or end is not numeric?
Could I also hear an answer to this error? I'm in a similar situation and curious about how it was resolved.
I recall a issue recently where the input contained the same sample repeated, GenVisR does not perform this type of QC check. Can you test this? Otherwise to debug try just two samples and see if it still errors
Hi,
I am trying to construct frequency plots for copy number data using cnFreq but I received an error message saying the following:
My input file:![image](https://user-images.githubusercontent.com/51113418/58462078-6c305c00-8131-11e9-9244-bb5329a912da.png)
I am using GenVisR v. 1.16.0.
Is it also possible to stratify patients according to different groups and to create frequency plots for the same?
Thank you for your help.
Kind regards, Hanna