[BioC] limma: read.maimages possibility to warn the user?
usadel at mpimp-golm.mpg.de
Mon Jul 31 12:43:00 CEST 2006
when using read.maimages from limma with a "broken" file (tabs replaced
by ":", two extra tabs added at the end of row e)
limma reads the table fine
But I get NA values added in all columns thus changing the order of
probes in this particular arrayfile
[6,] NA <-
Marray on the other hand, complains using the following syntax and
refuses to read in the offending file.
"Error in scan(file = file, what = what, sep = sep, quote = quote, dec =
dec, : line 5 did not have 5 elements"
Even though I appreciate, that limma reads the data fine without the
usual read.table hazzle and realize that the data should have been
checked before reading it in anyway, I think at least a little warning
could greatly help.
But maybe I missed something important (not being a two color type anyway)?
(The broken files result from an MS Excel export and this happens on
R2.2 with limma 2.4.13 and on R 2.3.1 with limma 2.6.2)
Björn Usadel, PhD
Max Planck Institute of Molecular Plant Physiology
System Regulation Group
Am Mühlenberg 1
Tel (+49 331) 567-8114
Email usadel at mpimp-golm.mpg.de
More information about the Bioconductor