Hello,
there are a number of packages that could help you with the
normalization. For example, have a look whether the function
"normalizeByReference" from package "tilingArray" is useful for you.
Once you have an ExpressionSet of normalized data, the packages Ringo
and ACME may be useful for identification of ChIP-enriched regions.
Best regards,
Joern
Yanqin Yang wrote:
> Hello,
>
> I have four CHIP-on-chip datasets on affymetrix mouse promoter
1.0 R array, which are duplicate for both target protein and control
group. By using makePlatformDesign and oligo packages, I have
successfully read in the *.cel files. Now, I am stuck for the next
step. Which package should I use for normalization and further
statistic analysis? This is my first time dealing with CHIP-chip
tiling array. Would anyone kindly help me out?
>
> Really appreciate your help!
>
> Yanqin
>
>
