illumina microarray gene Technology

Question

[Kritika]

Hi everyone I will be given certain illumina micro array gene expression data in couple of weeks. I am new to illumna microarray gene expression analysis. So I need to clear certain basics. I read certain research paper where they mentioned for analysis purpose lumi and beadarray from bioconductor is mostly used. My question is for raw data what will the format which I will get ? I means what is the format or files are required for illumina microarray data analysis. Also when I was reading about "lumi " I came accross example.lumi which is used in lumi tutorial my question is how I will get this .lumi data. Any one please help. Thanks

[Amitm]

Hi,

It is not clear what you mean by 'data' here. Because it could be either the raw format that is spit out by the array scanner as image files (I think Tiff format), or do you mean the background-normalized signal intensities that can be exported from the Illumina GenomeStudio software.

Few pointers -

1. The raw format are image files
2. You can use the Illumina GenomeStudio software which you would have license to if you are doing the experiment on-site. You might not if you have out-sourced it.

GenomeStudio would accept the image files and would allow you to extract signal intensity ratios, after background correction. In fact you can do the whole analysis => between array normalization and finally differential expression, in GenomeStudio itself.

So per se you wouldn't require to go to R. But if you want to use the methods in R for Illumina array then there are two entry levels -

A) beadarray package - You go here if you want to start from scratch i.e. from the image files. The output would be signal intensities (which you can get from GenomeStudio as well)

B) lumi package - You go here if you already have the signal intensities exported from the GenomeStudio software (or beadarray package above).

The example.lumi is an example dataset contained within the lumi package. If you read the documentation here, its not difficult to follow. The lumi package documentation gives enough details about the data format it needs.

[poisonAlien]

What arrays are you using ? Illumina beadarrays (HT12) ?

Answer 1

[Kritika]

My question was for lumi ( for lumiQ , for normalization and further analysis) what input files I need to give.