[BioC] Stuck with Yeast Tiling Array

[Richard Harrison]

Dear All,
I am having problems trying to analyze some genomic tiling arrays  
that i have done using s.cerevisiae reverse tiling arrays. Can anyone  
help on some/all of these issues please?

I am trying to use the tilingArray package and the davidTiling packages

1) I  load my arrays in using the following commands:

cels= dir(pattern=".CEL")
richard  = readCel2eSet(cels)

this renames my arrays to "1" and "2". How can i rename these to  
their original names?

 > dim(richard)
Features  Samples
6553600        2
 > sampleNames (richard)
[1] "1" "2"
 >


Second it puts them in one column. How can i make this two  
columns....or more (see below)

 > library(davidTiling)
 > data("davidTiling")
sampleNames(davidTiling)
 > sampleNames(davidTiling)
[1] "09_11_04_S96_genDNA_16hrs_45C_noDMSO.cel"
[2] "041119_S96genDNA_re-hybe.cel"
[3] "041120_S96genDNA_re-hybe.cel"
[4] "05_04_27_2xpolyA_NAP3.cel"
[5] "05_04_26_2xpolyA_NAP2.cel"
[6] "05_04_20_2xpolyA_NAP_2to1.cel"
[7] "050409_totcDNA_14ug_no52.cel"
[8] "030505_totcDNA_15ug_affy.cel"




Thanks,
Richard