Dear list,

I got a weird problem when I tried to use read.table to import my data
matrix for drawing heatmaps. I have two different txt files generated in
same way. The first one worked fine when imported into R using code1(listed
below), and the second one got lots of warning messages using code2 (codes
are almost same but file names changed). I have checked the whole process
again and again, these two files do have no obvious difference except the
genes.  I have already searched the google and maillist but still have no
idea what's wrong.
Can anybody give me some clues? Thank you very much!!

## code1
hmap1 <- read.table("For heatmap_annot_limma_P0.001_txn.f.txt", header=TRUE,
sep="\t", row.names=1)
eset1 <- new("ExpressionSet", exprs=as.matrix(hmap1)) ; dim(exprs(eset1))

### got correct dim as original matrix --  [1] 416   4

## code2
hmap2 <- read.table("For heatmap_annot_limma_P0.001_txn.S.txt", header=TRUE,
sep="\t", row.names=1)
eset2 <- new("ExpressionSet", exprs=as.matrix(hmap2)) ; dim(exprs(eset2))
          Warning message:
                             In scan(file, what, nmax, sep, dec, quote,
skip, nlines, na.strings,  :
                             number of items read is not a multiple of the
number of columns


All suggestions are really appreciated!!
Hui-Yi

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