Question: Missing normalized x, normalized y, baf and logrrratio values
0
gravatar for dharia.priyadarshani
17 months ago by
dharia.priyadarshani0 wrote:

Hi, 

  I am trying to load intensity files and bl files using GWASTools. I got the following error: 

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  scan() expected 'a real', got '"0.9958377"'

 

I checked my data and realized that my variables are a string. 

1. I am not sure if being a string variable is the issue for this error. 

2. What do I denote missing values in normalized x, normalized y, baf and logrrratio values, so intensity and baf files can be uploaded. 

 

Thank you for your help.

Best, 

Priya

gwastools • 249 views
ADD COMMENTlink modified 17 months ago by Stephanie M. Gogarten670 • written 17 months ago by dharia.priyadarshani0
Answer: Missing normalized x, normalized y, baf and logrrratio values
1
gravatar for Stephanie M. Gogarten
17 months ago by
University of Washington
Stephanie M. Gogarten670 wrote:

1. I am not sure if being a string variable is the issue for this error.

Yes, it is. You will need to remove the quotation marks around the intensity/BAF values.

2. What do I denote missing values in normalized x, normalized y, baf and logrrratio values, so intensity and baf files can be uploaded.

The createDataFile code calls read.table, so it follows the rules for missing values in that function. Either "NA" or a blank field indicates a missing value for non-string data.

ADD COMMENTlink written 17 months ago by Stephanie M. Gogarten670
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 214 users visited in the last hour