Question: Using limma for Differential Expression test
0
gravatar for v82masae
2.3 years ago by
v82masae120
v82masae120 wrote:

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    ....
.
.
.

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?

ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.3 years ago by v82masae120
1

Have you tried following an example from chapter 17 of the limma tutorial? That got me through the same situation..

ADD REPLYlink written 2.3 years ago by fanli.gcb660
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1844 users visited in the last hour