Question

Is it possible some statistical evaluation with a few replicates and one control in microarray data analysis in r

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svlachavas ▴ 830

@svlachavas-7225

Last seen 13 months ago

Germany/Heidelberg/German Cancer Resear…

Dear All,

i started preprossesing a small affymetrix microarray dataset. Due to some technical problems, i aquired only one control sample and 4 different samples representing 4 different biological susbstances as treatments(5 CEL files total). Except from quality control, could i use some method for DE expression, because due to the number and the phenotype of the data, i think it is not possible, even with limma. So my question is should i wait for gaining some more samples or there is some alternative? i have heard of rank products algorithm but i have never used it.

r bioconductor affymetrix differential gene expression • 1.1k views

ADD COMMENT • link updated 9.7 years ago by James W. MacDonald 67k • written 9.7 years ago by svlachavas ▴ 830

score 2 · Answer 1 · 2015-02-20

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 10 hours ago

United States

If you are going to be getting more replicates, the best idea would be to wait.

ADD COMMENT • link 9.7 years ago James W. MacDonald 67k

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Possibly, but the problem is that because i have to give a small report about this dataset and the other replicates will delay for the time being, i wonder if i just perform only a quality control and suggest that any statistical test based on these samples would be inappropriate ?

ADD REPLY • link 9.7 years ago svlachavas ▴ 830