Transcriptome Analysis Console (TAC) vs R Bioconductor

Question

[Juan Cordero]

Dear comm,

I've seen many molecular biologists usually perform a primary analysis of Affymetrix microarray data with TAC software provided by Affymetrix. However, such automatic analysis does not seem quite reliable for me. Should I trust results from TAC, or should I analyse such data instead by doing the whole process with Bioconductor? I suspect you may easily get misleading outputs with TAC...

Thanks

Answer 1

[svlachavas]

Generally Bioconductor group (http://www.bioconductor.org/help/workflows/arrays/) has many easy pipelines for performing analysis of Affymetrix microarray data, and also many tutorial and MOOCs are on Coursera and Edx. Personally, with a little practice in the beginning, R is wonderful and you have full control of your analysis. To be honest, i dont vote against TAC, but i personally prefer using many different packages and methodologies through R than automated analysis. On the other hand, if you dont wish to have a full deep crush into programming and just want to use an easy and basic program or tool to just perform an analysis, then you should do so-and yes i believe that TAC would produce reliable results. I only have used TAC with specific Affymetrix microarray platforms, such as HTA 2.0, which are not supported by other packages due to its complex nature. So, it is up to you what you use and how to interpret your results.

Best,

Efstathios