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