Tiling Array Analysis

Question

[Litali]

Which software is recommended to analyze tiling array data for expression analysis?

Answer 1

[Thaman]

You can check out

• cisGenome and for analyzing tiling array data you can read the manual
• Tilescope which is more handy but doesn't seem to work right now.
• If you want to analyze through R/Bioconductor then Starr package

[Litali]

Thank you, I see Starr is for affymetrix, I need for nimblegen tiling array for a novel genome expression,,,

Answer 2

[Rm]

I would recommend NTAP - NimbleGen Tiling Array Analysis Package.

[Bdv]

I saw it is for Chip-chip analysis, is it different from expression analysis?

[Rm]

You can use it for exp analysis too, with little tweeks