[BioC] flow cytometry data

[Nolwenn Le Meur]

David martin wrote:
>
> 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 ?
I do not think you should normalize your data at that point.
If any normalization would be required I think that it should be done on 
the raw data to correct for some bias identify by quality assessment 
analysis.

Here you should have a look at the distribution of your data to choose 
between a parametric or non-parametric test (many you can find in R or 
BioC).

Nolwenn

>
>
>
> 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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-- 
Nolwenn Le Meur, PhD
IRSET - Institut de Recherche en Sante-Environnement-Travail. 
INSERM/IRISA - Equipes INTEREST/Symbiose 

Universite de Rennes I
Campus de Beaulieu
35042 Rennes cedex - France
Phone: +33 2 99 84 71 17
Fax: +33 2 99 84 71 71
E-mail: nlemeur at irisa.fr
Website: http://www.irisa.fr/symbiose/nolwenn_le_meur