1. What is tiling array, and what's the difference of tiling array with ChIP-chip?

Benefit from the technology development, the probes/oligos can be simultaneously put onto a single microarray is increasing dramatically. Differ from the traditional microarray which usually only represent the gene coding region (for gene expression detection) or promoter region (Transcription Factors binding events detection), Tiling array covers the whole genome with tiled probes along the whole genome (sometimes are not real tiled, but very dense). In another words, there is no discrimination in the design of probes for tiling array, we choose as many as possible probes from the beginning to the end of each chromosomes existed in a cell so that it can provide a more integrated picture about the RNA transcription, TF binding, DNA methylation or histone modifications.

Many applications of tiling array adopt a protocal called ChIP (Chromatin ImmunoPrecipitation) to collect the samples needed for the hybridization onto the tiling array, those application are usually called ChIP-chip (first ChIP is the abbreviation for Chromatin ImmunoPrecipitation, while the latter one is indicating the tiling array used). So even though many of the tiling arrays are used for ChIP-chip experiments, not all of the tiling array are used for ChIP-chip, the RNA transcription and DNA methylation detection is using traditional methods to collect the samples instead.

The main commerical tiling array products are from Affymetrix, NimbleGen and Agilent. But due to the arising of next generation sequencing technology, more and more experiments are switching from tiling array to sequencing, our software is able to be applied for sequencing result as well.

2. What NTAP is designed for?

NTAP is developed in the progress of the histone modification research in Rice (Oryza sativa), an important crop species. So the package includes function from the raw data normalization to post-processing tools, more specifically, summarize and plot the distribution of histone modification level along the specified region so that user can compare the distribution between different conditions or different types of genes (high versus low expressed genes).

The tiling array we used (Plant Cell2008) is not dense enough, which limits our choice of algorithms. Many of the proposed methods like HMM requires very dense design of tiling array. If you are using very dense tiling arrays, you can choose to use the fancier algorithms and then plot your results using our package, or you can still use our package for your analysis. The true signals will stand out anyway.

NTAP is written in R and used limma package from the bioconductor project.

3. Can I use NTAP for expression detection arrays?

Yes, you can. Actually our post-processing tools are separated from the pre-processing tools. You can use whatever pre-processing tools and only if you can convert your result into gff format, NTAP can plot the distribution for you.