Hello everyone, I'm used to DE analysis using RNA-seq data, but now I have to deal with microarray data.
I have this tabultated data:
Probe set 8688GM 8689GM 8692GM 8693GM 8694GM ...
AFFX-BioB-5_at 7,7463541031 7,4153280258 8,2151260376 8,3019447327 ....
AFFX-BioB-M_at 8,7242946625 8,3872909546 9,1244878769 9,2067680359 ....
AFFX-DapX-3_at 9,6434116364 9,1975746155 8,5922412872 10,1100711823 ....
AFFX-DapX-5_at 8,2542390823 7,8620843887 7,1700358391 8,5010471344 ....
AFFX-DapX-M_at 8,6828374863 8,5149002075 8,0686988831 9,3369913101 ....
AFFX-LysX-3_at 6,051358223 6,2062387466 5,5821290016 7,1206626892 ....
AFFX-LysX-5_at 3,5149636269 3,3956513405 3,6194758415 4,5964984894 ....
AFFX-LysX-M_at 3,2489645481 2,9336781502 2,8604176044 3,3880860806 ....
AFFX-PheX-3_at 6,0353684425 5,2056517601 5,1288986206 6,2471790314 ....
AFFX-PheX-5_at 4,4866952896 4,5793194771 4,2034420967 5,2232532501 ....
AFFX-PheX-M_at 4,3788428307 4,2975893021 4,1539840698 4,7329955101 ....
AFFX-r2-Bs-dap-3_at 9,4406995773 9,0966424942 8,9008131027 10,305314064 ....
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With a total of 91 columns corresponding to 91 animals, and 6000 rows corresponding to each probe or gene hibridized in the microarray. These data belongs to another researcher who passed it to me, informing that those values are already normalized and ready to use for DE analysis. Within the 91 animals, they can be divided into 3 groups, lets call them group 1, group 2 and group 3. I would like to know what genes are differentially expressed when comparing groups 1-2, 1-3 and 2-3. I've been looking around and have found limma package to do so, but by reading some tutorials and manuals, I did not get a clear idea about how to construct the group matrix and fit the linear model to do the analysis over all the genes comparing two groups.
I managed to do a single gene comparison using a t-test but when dealing with all of them at the same time, I kept wondering how to do it.
Any help?
Have you tried following an example from chapter 17 of the limma tutorial? That got me through the same situation..