Microarray data analysis in R

Question

[smrutimayipanda]

Hii, I am looking for microarray data analysis pipeline in R language for single colour agilent data. Please help me in this. Atleast give me idea or some kind of R script for this analysis. Thanks in advance.

Answer 1

[Kevin Blighe]

This should permit that you 'get off to a good start': How to process (seems) Agilent microarrry data?

For more specifics, please refer to the limma manual.

There are likely many other workflows to be found online.

Kevin

[smrutimayipanda]

Yeah this link worked for me, but I need a detailed glimpse how this code is working. I want to know how this code is working as QC, background correction, normalization, etc. If you have link, please let me know.

[Kevin Blighe]

In that case, please read through the limma manual, and also the individual function manual pages. For example, to quickly access the manual for read.maimages(), I would type ?read.maimages.

[smrutimayipanda]

hii kevin, I need your help. Can you give me a R code for single-colour agilent microarray data? Including QC, normalization, differential analysis, multiple testing, etc. I have tried but failed in between.

[Kevin Blighe]

I am reluctant to just give code --sorry-- and neither can I, because you have not stated the exact type of data (the array version) that you have, nor anything about your experimental design. It would also help to elaborate on the specific parts where you encounter difficulty.

A search across the World Wide Web should give you enough information, and also using that information already provided here:

• How to process (seems) Agilent microarrry data?
• build the expression matrix step by step from GEO raw data
• limma manual, section 4.5: https://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf

[smrutimayipanda]

Kevin Blighe Can you please tell me whether I can use this same link for processing Agilent miRNA microarray data?