illumina ht 12 v4 data analysis

Question

[amin.ghareyazi]

Hi

I have a matrix of normalized microarray gene expression. probe-IDs are in rows and samples are in columns. I don't have any annotation files to pass to limma in order to start my analysis. I only know it is from illumina ht 12 v4 chip. Accession code refers to a GEO data that only covers a small subset of my data.

where can i find the annotations needed for limma? how should i use them?

Is there any way to analyze this dataset without annotation files?

Answer 1

[Gordon Smyth]

limma does not require annotation files to do the analysis, but of course without annotation you won't be able to interpret the probe-ids. To get gene symbols and and so on for the Illumina probe-ids, just go to the Illumina technical support page and download the manifest file for the Illumina HT-12 chip:

https://support.illumina.com/array/array_kits/humanht-12_v4_expression_beadchip_kit/downloads.html

[amin.ghareyazi]

thanks Gordon. but what if some of the probes I have are control probes? also I couldn't find any example for limma working without annotations. all I can find are examples that passes objects with annotations. can you give me at least a link to show me how it works?

[amin.ghareyazi]

And how should I use this annotation file? how can I pass it to limma with my data?