[BioC] nimblegen ChIP to chip array

[Ido M. Tamir]

On Tuesday 21 February 2006 17:25, ping zheng wrote:
> Hello everyone,
>
> I have never analyzed microarray data, I would like to use
> Biochonductor to analyze data provided by nimblegen. Method used was ChIP
> to chip
> array and data is provided in the following format
>
> *_ratio.gff, *_pair.txt, *_report.tab
>
> How can I use normalizeBetweenArrays or Loess function for the data
> provided by nimblegen in the format specified above?
> Can someone tell me what type of data is required for applying these
> functions?
> Does the data format vary from company to company like nimblegen and
> affymetrix?
>
> Thank you for your time and help
>
Yes the data format varies.
What I do is:
1) read out the .ndf and .pos file
2) read out the individual _pair.txt files
and reorder them by the ndf file.
3) crate an RGList out of the data
4) then you can use normalize away Within
and Between arrays as you wish.

Regarding the normalization:
After some discussion and tests
I also advise against using loess
for nimblegen data.
For other arrays (cDNA with large
fragments) I still don't know
what the best method (or even a good one)
is.

What nimblegen itself does for creating
your gff files (which contain normalized data)
is to basically subtract an average of the log2
ratios from all the values (like median normalization)
The average is calculated using a tukey
biweight.

best wishes
ido