Hello everybody I want to manually up-regulate some genes (a have a list of genes) as compare to other in my normalized gene expression matrix . i am doing this just by increasing the values. I am not sure what number i add in the intensity value of my gene of interest,so that it become up regulated in my normalized gene expression matrix kindly give me some suggestion on this. Thank you With kind regards Reema Singh [[alternative HTML version deleted]]

Hi, On Tue, Mar 20, 2012 at 11:13 AM, Reema Singh <reema28sep at="" gmail.com=""> wrote: > Hello everybody > > I want to manually up-regulate some genes (a have a list of genes) as > compare to other in my normalized gene expression matrix . i am doing this > just by increasing the values. I am not sure what number i add in the > intensity value of my gene of interest,so that it become up regulated in my > normalized gene expression matrix > > kindly give me some suggestion on this. It might help to explain a bit about what you're trying to accomplish with this exercise. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

On Tue, Mar 20, 2012 at 9:09 PM, Reema Singh <reema28sep at="" gmail.com=""> wrote: > Hi Sean > > Thanx for your reply. Actually in my Ph.d i am working on micro array > meta-analysis. First, I want to check that whether the differentially > expression protocol which i am using is able to pick those genes as > upregulated genes which i have manually up-regulated ( by just adding some > number in the gene intensity of those genes) in normalized gene expression > matrix or not. > > In order to? manually up-regulate a gene, i am doing this:- > > gene A = 0.4820938 (log intensity) + 2 (some number) = 2.482094 > > Adding some positive number to log intensity of particular gene ,this is > what i mean by manually up regulating a gene. But i am not sure about it, i > tried to search it on internet but didn't find much. Hi, Reema. I think the question both Steve and I are trying to answer is different than the one you are asking. What is the big picture? Why do you want to "upregulate" a gene? How does meta-analysis come in? What are you going to do with your new, altered dataset? Sean > Thankyou > > Reema Singh > > On Tue, Mar 20, 2012 at 9:37 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> >> >> >> On Tue, Mar 20, 2012 at 11:13 AM, Reema Singh <reema28sep at="" gmail.com=""> >> wrote: >>> >>> Hello everybody >>> >>> I want to manually up-regulate some genes (a have a list of genes) as >>> compare to other in my normalized gene expression matrix . i am doing >>> this >>> just by increasing the values. I am not sure what number i add in the >>> intensity value of my gene of interest,so that it become up regulated in >>> my >>> normalized gene expression matrix >>> >>> kindly give me some suggestion on this. >>> >> >> Hi, Reema. >> >> You will need to provide a bigger picture of what you are trying to do. >> ?Keep in mind that, generally speaking, one cannot use a microarray to say >> that one gene is expressed more than another. ?Microarrays are good >> measuring relative gene expression across samples but not good at measuring >> absolute gene expression, so comparing the expression of one gene to another >> using microarrays is not straightforward and is not a typical microarray >> analysis. >> >> Sean >> >