[BioC] flow cytometry data
David martin
vilanew at gmail.com
Thu Dec 3 12:20:45 CET 2009
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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>
>
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