analysis of tiling array

[litali]

Anybody knows which software can fit for analysis for nimblegen tiling array?
after I have the raw data from nimblescan , which further software can fit?

[smarthey]

Hello,
which kind of analysis ?
for CGH or DNACopy analysis you can use the Nimblescan software.
for expression I used a custom pipeline based on perl and R. I didn't try Niblescan software for this but I think he can do that. you should look at the documentation

http://www.nimblegen.com/products/software/

[litali]

tiling

It is expression analysis. I think nimblescan can only produce raw data and then I need a custom pipeline or 3rd party software, so I wanted some specifi recommendations,,,

[smarthey]

I agree with you, the main function of Nimblescan is the quantification.
However, it has a part "analysis" in which you can make the normalization step (specific for Nimblegen chips), the segmentation step, etc....
It will be very fast to look at the documentation here and check if it can make what you want:

https://www.nimblegen.com/products/lit/NimbleScan_v2p6_UsersGuide.pdf

I don't know if a free 3rd party software exist actualy, but if you find one, please put the name here. That can help me for future ;-)

[simonandrews]

We wrote ChIPMonk to deal with this kind of data. It used the combined pair file from Nimblegen arrays and let you do a load of different types of analysis. It's not been updated for a while as we've moved on to ChIP-Seq these days but it should still work OK.

[Wolfgang Huber]

Litali,

Bioconductor provides a comprehensive set of building blocks for your own custom analysis. The "Ringo" package may be of interest for data import and visualization of Nimblegen data. I don't think there is a standard way of analysing tiling array expression data, some ideas are in the "tilingArray" package and accompanying papers.

Furthermore, the "oligo" package has relevant functionality, and a vignette "Analysis of NimbleGen Expression Data with the oligo Package" by Benilton Carvalho.

To use these tools, you'll need to invest some time into learning the R language, but that tends to be a worthwhile investment.

Best wishes
Wolfgang