Hello everyone!!
Can anyone suggest a free good software or bioinformatics webpages for miRNA micro-array analysis where representative schemes are produced in a way that summarizes the nature of samples or experimental design ( i mean in terms of the sampling for repeated measures or segregated genes and so on)??
thanks
R with Package Bioconductor is very good. A good place to start is S. Knudsen, Cancer Diagnostics with DNA Microarrays, Wiley. There are sample programs in Chapter 10. I would highly recommend this book. Knudsen's earlier books are also good.
Dear David
thanks a lto for your response, useful reference, but i was thinking what sort of snalysis you are referring to?? i am not so much familiar with R and will be attending a course soon it will be nice to know what analysis you are refereeing to
was thinking of IPA if it is relavant
Thank you. I have to admit my ignorance here. I have only worked with DNA arrays so whatever is different with RNA arrays is unknown to me. However the programs in the book include PCA, ANN, Classification, Survival Analysis and some others from Bioconductor as well. If you are just starting out with R, I think that it is helpful to have some of these commonly used methods available as almost off the shelf programs. There are also references to test data sets that allow you to try out the programs. In our work with the DNA arrays and AL Leukemia, we mostly used ANNs. I am unfamiliar with QIAGEN's IPA even though we have recently been working with SNPs. I would expect the QIAGEN people would be able to guide you with IPA. The link below may be of some help although you probably already are familiar with it. I hope this helps a little bit. Best wishes.
http://www.ingenuity.com/
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