[BioC] Manually upregulate a gene

[Sean Davis]

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
>>
>