[BioC] flow cytometry data

[David martin]

Sorry to ask but what are the tests ??


Nolwenn Le Meur wrote:
> 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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> 
>