I would like to examine the microarray database (I am using Geo) to examine the differential expression of one gene in a diseased group compared to the healthy group. typing in the and The list shortens to 18 items searches; I then want to probe this to see if there is a significant difference in the gene expression between the two. I have hit on the individual search and asked to compare groups but then it takes me to a all the genes which have been (I assume up or down regulated) in that sample rather than the genes that I am interested in. And even then, there is no statistical output. I have no real experience in microarrays so I apologise if these are trivial questions - I am trying to show that the data is helpful towards our hypothesis. However, I am very aware that there is huge potential to misinterpret and handle the array data extremely badly. I truly hope someone can help! Thanks, Vani, Clinical PhD student, Imperial College.
Search your query on GeoDatasets(http://www.ncbi.nlm.nih.gov/gds/). ex alzheimer
Click on selected dataset, new page will open containing dataset information.
Click Reference Series-- GSE----- (Series accession number). ex GSE56899.
Now click on "Analyze with GEO2R". its a inbuilt R script at GEO
Follow this tutorial for further analysis "http://www.ncbi.nlm.nih.gov/geo/info/geo2r.html"
If you want information for a single gene then simply use "http://www.ncbi.nlm.nih.gov/geoprofiles", search for your Gene of interest .
Hi!
Thanks to both of you! I am basically looking at expression of il1b during active tuberculosis (to compare with uninfected or latent controls) in blood or any other sample available. So Rakesh, writing in tuberculosis in the first link will give me 5000 results so its too broad; on the other hand tuberculosis il1b gives 1 results which I know is not correct! For geoprofiles, I can write tuberculosis and il1b and it gives me 18 results (I am not sure if this is too less however) - but I am then not sure how to analyse this further?
Am I making sense? I do appreciate the help! Vani
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