[BioC] flow cytometry data

David martin vilanew at gmail.com
Thu Dec 3 10:59:49 CET 2009


I have tested different cell surface markers on a sub population of 
monocytes. The matrix below shows a small snapshot of the different cell 
surface markers tested (cdA,cdB,cdC..) in different monocytes of 
patients that are either normal patients or treated patients.
The values are the geomtrical mean obtained from the flow. They are 
log10 values.
The question here is to identify markers differentually expressed in the 
monocytes subpopulation between normal patients and control patients.

marker	normal	normal	treated	treated
cdA	-5.27	1.48	-1.28	-1.01
cdB	-5.31	-1.89	9.31	1.01
cdC	4.12	8.1	8.16	3.6
cdE	30.44	11.59	3.39	14.64
CD11c	5.36	-1.48	-5.7	-4.44


Do i hve to normalize the data first ? I though this was already done by 
the instrument ? i might be wrong. Any idea ?



Nolwenn Le Meur wrote:
> Hi David,
> 
> I am not such I see what are the data you are manipulating. What is the 
> experimental design and biological question(s)? What represent the fold 
> change you want to compute? What are the rows and columns in your log10 
> data matrix?
> 
> For data analysis of cell-based assay, you might also want to have a 
> look at the cellHTS2 package.
> 
> Best,
> Nolwenn
> 
> David martin wrote:
>> Hi,
>> I've recently got some data from the lab coming from flow cytometry.
>> I have the log10 values corresponding to the geometrical mean (not the 
>> flow cytometry files).
>>
>> Basically i would like to start from that matrix and compute the fold 
>> changes. I'm not sure which test is most suitable as not sure which 
>> sitribution the data follows , gaussian ??? could anybody suggest how 
>> to move on from the log10 data matrix ? Any paper or tutorial .
>> I have already looked at the flow packages within R but most of them 
>> deal with gating and scaling the raw data, but not how to compute fold 
>> changes
>>
>> thanks for any help,
>> david
>>
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> 
>



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