Entering edit mode
Björn Usadel
▴
250
@bjorn-usadel-1492
Last seen 10.2 years ago
Dear list,
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
table:
:R:G:RB:GB
a:1:2:0.5:0.5
b:2:4:1:1
c:3:6:1.5:1.5
d:4:8:2:2
e:5:10:2.5:2.5::
f:6:12:3:3
g:7:14:3.5:3.5
code:
RG<-read.maimages(files="test.txt",
path="C://cpan//",columns=list(Gf="G",
Rf="R",
Gb="GB",
Rb="RB"
))
But I get NA values added in all columns thus changing the order of
probes in this particular arrayfile
$G
test
[1,] 2
[2,] 4
[3,] 6
[4,] 8
[5,] 10
[6,] NA <-
[7,] 12
[8,] 14
Marray on the other hand, complains using the following syntax and
refuses to read in the offending file.
RG2<-read.marrayRaw(fnames="test.txt",path="C://cpan//", name.Gf="G",
name.Rf="R",
name.Gb="GB",
name.Rb="RB"
)
"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)
Cheers,
Bj?rn
--
-+-+-+-+-+-+-+-+-+-+-+-
Bj?rn Usadel, PhD
Max Planck Institute of Molecular Plant Physiology
System Regulation Group
Am M?hlenberg 1
D-14476 Golm
Germany
Tel (+49 331) 567-8114
Email usadel at mpimp-golm.mpg.de
WWW mapman.mpimp-golm.mpg.de