I am trying to do the analysis with DAVID but their is some problem with the software. Please suggest software which is freely available.
Hi Deepa,
David normally works well and is the one I use. But also have Panther http://www.pantherdb.org/ or Reactome http://www.reactome.org/, depending on the type of analysis you want to do. Anyway, you can try to search another tool that better fits your requirements here: http://omictools.com/.
I hope these information helps you.
Good luck!
From the web site, it does not appear that the underlying database in DAVID has been updated in 4 to 5 years. If it really is that long out of date, and especially as it does not seem to be actively maintained nor updated any longer, I honestly would use another resource like those mentioned. Ontology information is not static so if a resource is truly deprecated than it is really no longer useful.
usually, annotation of the probes can be done in R with the plat-from specific annotation packages available from bioconductor(hgu133plus2.db etc). As for some uncommon platforms(such as agilent as well as illumina HT series), annotation files can be found via google or the manufatures official website. what we have to do is just read them into R and match those probes accorindg to probeIDs, although it is a liitle cubersome.
for clustering analysis of microarray data, I have used heatplot in made4 R package which do both sample and gene clustering and plot a heatmap of the expression value. WGCNA package also has a clustering function which runs faster than hclust when the size of the input is very huge.
good luck.
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