Which Method Do You Use To Find The Differently Expressed Genes In Microarray?

Question

[C Shao]

Hi,

There are different methods in handling microarray data, such as SAM, Rank Products, limma, or simple student test... I am just wondering which methods do you prefer in finding differently changed genes? Personally, I use student test or anova, sometimes with SAM.

Thanks,

Answer 1

[Steve Lianoglou]

Limma is the Α and the Ω in my book.

Answer 2

[Larry_Parnell]

We sometimes use SAM. On our last expt., involving miRNAs, the differentially expressed genes were detected using a simple T test. We had just three replicates.

[toni]

t-test with three replicates is not applicable. Some distributions have to be calculated and with 3 points, it's not possible. You 'd rather use a wilcoxon (non-parametric) test whn dealing with small datasets.

[Larry_Parnell]

Well, I cannot argue on my colleague's behalf. That said, in brief, with his 3 expression data points per microRNA he estimated the variance, and combined with n=3 ran the T test. He acknowledges that this is not ideal but states that it is indeed possible.

[C Shao]

When I deal with data from on 3 samples experiments (shotgun ms data), I used PLGEM. The results seemed fine, so it may be an alternative.

Answer 3

[Pasta]

Anova with a FDR

[Houkto]

in your case of small number of replicates, i think RankProducts (non-parametric test) would be more suiable. However, there is no goldstandard test if you have enough time why not try a number of parametric tools and non-parametric tools and then take the intersect of both which ultimatel that most reliable source of significant differently expressed genes.