Hello everybody. I'm new using R, Bioconductor and HTA microarrays.
I have tried to find some step by step guide or document to analyze HTA2.0 microarrays, but I have not found anything. All I found was this article: "An end to end workflow for differential gene expression using Affymetrix microarrays" , which applies it to other types of microarrays. Could the same steps be used?
Thank you very much and sorry for the inconvenience.
The HTA arrays are in some sense the same as any other. There are probes that measure things and you can combine them to generate an estimate and then see if the estimated values are different between groups. So in that sense you can analyze the HTA arrays just like in the End to End workflow.
But that's not really the intent Affymetrix had in mind when they designed those arrays. The stated intent is that people would be able to infer differential transcript abundance, and there are a lot of specialized probes on the array that are intended to help one with that task. Affy developed a software called Transcriptome Analysis Console that is specifically designed to do that sort of analysis, and you might take a look at that. Unfortunately that's the only software that I know of that is intended to do that specialized analysis.
So if you have some HTA arrays and just want to do differential expression, you could emulate the End to End workflow. If you plan to use the HTA arrays for their intended use you will need TAC.
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Thank you James. I'll take a look at that program. Anyway, my goal is to make a differential expression. For this purpose, what do you recommend, R/Bioconductor or TAC?
I would personally default to R/Bioconductor because you can actually know what you are doing, which is not necessarily true with TAC. But I can't make a recommendation for you. As the analyst you will have to decide for yourself what you think is the way to go.
Thank you again James. I will follow your advice. Now I will try to follow the steps of the article.
Hello Dr. @James
What I have been able to verify is that when I make an analysis with "TAC", many probes appear without gene annotation. So what I have done is to export the intensities given by TAC using SST-RMA and annotate it in R with your packages. The DEG was then done using limma.
Is this correct? Thank you in advance.
I cannot help you with that. Maybe @james-w-macdonald-5106 can help you.