User: Nolwenn LeMeur

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Posts by Nolwenn LeMeur

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Answer: A: flowCore - how to see the marker names?
... Hi Anne, The parameter annotation of a flowframe is stored in an annotated dataframe. You can access the information using the pData function: pData(parameters(FCS)) see the flowFrame-class man page for more details Nolwenn Anne wrote: >Hi, > >I am having problems in finding the mar ...
written 11.0 years ago by Nolwenn LeMeur140
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Comment: C: Reading Agilent files using read.maimages
... Hi Steve, I have download the files and it seems that each file has its own header. By this I mean that a prefix has been add to each standard column. For example, for file "E-MEXP-668-raw-data-921408043.txt" every column start with "H_C1 A_mock A and B/" whereas in file "E-MEXP-668-raw-data-921408 ...
written 11.8 years ago by Nolwenn LeMeur140
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Answer: A: Extract raw numerical data from a flowframe?
... Hi Matt, To access the data in a flowFrame object you have to use the exprs() function: exprs(fs[[1]])[,1] or exprs(fs[[1]])[,"FSC.H"] This method is explained in the vignette but it is true that no example is given. We will fix that. Thanks Nolwenn M. Jankowski wrote: >Hi All, > >I've ...
written 11.8 years ago by Nolwenn LeMeur140
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Answer: A: working with prada objects
... Florencio Gonzalez writes: > > Thank you for the information. I'll give a try the new package. Just a > question about drawGate. > How can i get two or more populations from a file with the same drawgate > command? I see an option when creating the gate for combine the gating with & ...
written 12.1 years ago by Nolwenn LeMeur140
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Answer: A: working with prada objects
... Florencio Gonzalez writes: > > Hello, I?m new to bioconductor. I need to work with events from cytometer > data. I have to get the region of interest form drawGate and then work with > the events that are into the region selected. How can I access this events? > because drawGate cre ...
written 12.1 years ago by Nolwenn LeMeur140
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Answer: A: rflowcyt - read.series.FCS function
... Hi Jab, Thanks you for using rflowcyt. I have created the plotdensity.FCS function to perform some data quality assessment on 'raw' data but I believe you can use it on gated data. Depending on your gating approach, I think you can still read all your files at once with the read.series.FCS functi ...
written 12.8 years ago by Nolwenn LeMeur140
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rflowcyt and prada questions
... Hi Andras, Just a quick note to let you know that I've made some progress but I have not solved the problem yet. The problem comes from the $DATATYPE where in FCS2.0 the data are stored as integer (I) and in FCS3.0 as single float precision (F). I have also tried to read the files with prada and h ...
prada rflowcyt written 13.0 years ago by Nolwenn LeMeur140
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Newbie 'rflowcyt' question; problem loading facscan256.fcs (fwd)
... Hi Ulrik, We don't think that setting the locate globally is a good idea as it might interfer with other programs. I will make sure that the locate is checked at the beginning of the reading function and will add a warning message in case of incompatibility. Thanks for pointing out that problem, ...
rflowcyt written 13.0 years ago by Nolwenn LeMeur140
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Comment: C: Newbie 'rflowcyt' question; problem loading facscan256.fcs
... Hi Ulrik, I was not able to reproduce your error. However I have modified the read.FCS function. Could you test the new package ? You can find the new source at: http://bioconductor.org/packages/1.9/bioc/html/rflowcyt.html Have you tried with your own dataset? Nolwenn Ulrik Stervbo wrote: >H ...
written 13.0 years ago by Nolwenn LeMeur140
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Answer: A: The proper way of analysisng FACS-data; Question off topis?
... Hi Ulrik, I'm far from being an expert in analysing FACS-data but I can suggest you some tools implemented in rflowcyt (see the vignette): - you should use visualization tools (e.g. ECDF plot, density plot) to assess the quality of your replicates and verify the reproducibility of your experiment ...
written 13.0 years ago by Nolwenn LeMeur140

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