Question: Missing normalized x, normalized y, baf and logrrratio values
0
17 months ago by

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.

Best,

Priya

gwastools • 249 views
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
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.