[Bioc-devel] read.maimages, limma

Dear Laurentiu,

Thank you for alerting me to this problem, and thank you for providing your 
input file (off-line) which was essential for tracing the problem.

The error is caused by a new "feature" of the scan() function in R base. 
The NEWS file for R 2.1.0 says

     scan() has a new argument 'allowEscapes' (default TRUE) that
         controls when C-style escapes in the input are interpreted.
         Previously only \n and \r were interpreted, and then only
         within quoted strings when no separator was supplied.

The new behaviour has been made the default behaviour, surprisingly, which 
I think will have the effect of breaking most existing code which uses 
scan() to read delimited text files. The problem occurs when the text 
includes backslashes, such as Windows style file paths, which are now at 
risk of being interpretted as end of lines markers or other control characters.

I will post a fix within 24 hours to the Bioconductor development site as 
limma 1.9.1. The obvious fix will make limma dependent on R 2.1.0.

Gordon

Hi everyone,

I am using R.2.1.0 with limma 1.8.18 to read a "quantarray" .txt file.

RG <- read.maimages(file,source="quantarray")

Error in "[.data.frame"(obj, , columns$Rf) :
        undefined columns selected

The same data with the previous version of R (2.0.1) was working fine.
Does anyone have a suggestion?

Laurentiu

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