Question: Merging various panel for flow cytometry
0
gravatar for TEXTORIS Julien
6.7 years ago by
TEXTORIS Julien160 wrote:
Hi all, I'm quite new to flow cytometry, since i have mostly perfomed transcritionnal analyses before. I discovered the flowCore, flowViz, flowXXX packages in bioconductor and found it amazing. I have a series of data with two different panels (tubes) for each patient. As there are some common markers in both panels, i was wondering if i could merge the two into a single flowSet with more channels. In details : - for panel A I have SSC, FSC, CD45, CD3, CD4, CD8, HLA-DR - for panel B I have SSC, FSC, CD45, CD3, CD5, CD19, CD16 I would like to obtain a single merged-panel with : SSC, FSC, CD3, CD45, CD4, CD8, CD5, CD19, CD16, HLA-DR I was thinking that the dataset is composed roughly of a matrix with for each leukocyte (event, =row) a value for all channels above (columns). So, maybe it would be possible to try to clusterise by pairs the rows of panel A and those of panel B on common values of SSC, FSC, CD45 and CD3. The result dataset would take the mean of the common channels and then the single values for CD4, CD5, CD8, CD16, CD19, HLA-DR. I would be glad to have your comment on this before starting. Maybe it has already been done in some package, or maybe one would have a comment to take into accoutn before i start ? Thanks in advance. Julien -- Envoyé de mon ENIAC Julien Textoris, MD, PhD Laboratoire d'immunologie, UMR CNRS 7278, INSERM U1095 Faculté de Médecine Timone, Marseille +33 (0)4 91 32 49 71 Service d'anesthésie et de réanimation Hôpital Nord, Marseille +33 (0)4 91 96 55 31 [[alternative HTML version deleted]]
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ADD COMMENTlink modified 6.7 years ago by Jiang, Mike1.2k • written 6.7 years ago by TEXTORIS Julien160
Answer: Merging various panel for flow cytometry
0
gravatar for A H
6.7 years ago by
A H10
A H10 wrote:
Hi Julien, Unlike some transcriptional datasets, the parameters measured for each event (cell) in FCS are not necessarily correlated. Because of this, it is not always safe to assume that two events, 1 from Panel A and 1 from panel B, that have similar values of SSC, FSC, CD45 and CD3, are members of the same cell population and also have similar values of the non-common channels CD4, CD5, CD8, CD16, CD19, and HLA-DR. For example, in your data I speculate you would have a range of CD4 or CD8 values within a cluster of events that is defined by common values of SSC, FSC, CD45 and CD3. Regards, Andrew. -------------------- Message: 11 Date: Sat, 1 Dec 2012 11:25:36 +0100 From: Julien Textoris <julien.textoris@gmail.com> To: bioconductor@r-project.org Subject: [BioC] Merging various panel for flow cytometry Message-ID: <cadzdnvfxhwjclzsmmr7ygn5cgngf0lda+memw- n12kx_1aspjw@mail.gmail.com=""> Content-Type: text/plain Hi all, I'm quite new to flow cytometry, since i have mostly perfomed transcritionnal analyses before. I discovered the flowCore, flowViz, flowXXX packages in bioconductor and found it amazing. I have a series of data with two different panels (tubes) for each patient. As there are some common markers in both panels, i was wondering if i could merge the two into a single flowSet with more channels. In details : - for panel A I have SSC, FSC, CD45, CD3, CD4, CD8, HLA-DR - for panel B I have SSC, FSC, CD45, CD3, CD5, CD19, CD16 I would like to obtain a single merged-panel with : SSC, FSC, CD3, CD45, CD4, CD8, CD5, CD19, CD16, HLA-DR I was thinking that the dataset is composed roughly of a matrix with for each leukocyte (event, =row) a value for all channels above (columns). So, maybe it would be possible to try to clusterise by pairs the rows of panel A and those of panel B on common values of SSC, FSC, CD45 and CD3. The result dataset would take the mean of the common channels and then the single values for CD4, CD5, CD8, CD16, CD19, HLA-DR. I would be glad to have your comment on this before starting. Maybe it has already been done in some package, or maybe one would have a comment to take into accoutn before i start ? Thanks in advance. Julien -- Envoy?? de mon ENIAC Julien Textoris, MD, PhD Laboratoire d'immunologie, UMR CNRS 7278, INSERM U1095 Facult?? de M??decine Timone, Marseille +33 (0)4 91 32 49 71 Service d'anesth??sie et de r??animation H??pital Nord, Marseille +33 (0)4 91 96 55 31 [[alternative HTML version deleted]]
ADD COMMENTlink written 6.7 years ago by A H10
Thanks Andrew for pointing this out ! I understand the limitation clearly now. Regards, Julien 2012/12/1 A H <hillan141@gmail.com> > Hi Julien, > > Unlike some transcriptional datasets, the parameters measured for each > event (cell) in FCS are not necessarily correlated. > > Because of this, it is not always safe to assume that two events, 1 from > Panel A and 1 from panel B, that have similar values of SSC, FSC, CD45 and > CD3, are members of the same cell population and also have similar values > of the non-common channels CD4, CD5, CD8, CD16, CD19, and HLA-DR. For > example, in your data I speculate you would have a range of CD4 or > CD8 values within a cluster of events that is defined by common values of > SSC, FSC, CD45 and CD3. > > Regards, > Andrew. > > -------------------- > Message: 11 > > Date: Sat, 1 Dec 2012 11:25:36 +0100 > > From: Julien Textoris <julien.textoris@gmail.com> > > To: bioconductor@r-project.org > > Subject: [BioC] Merging various panel for flow cytometry > > Message-ID: > > <cadzdnvfxhwjclzsmmr7ygn5cgngf0lda+memw- n12kx_1aspjw@mail.gmail.com=""> > > Content-Type: text/plain > > > > Hi all, > > > > I'm quite new to flow cytometry, since i have mostly perfomed > > transcritionnal analyses before. I discovered the flowCore, flowViz, > > flowXXX packages in bioconductor and found it amazing. > > > > I have a series of data with two different panels (tubes) for each patient. > > As there are some common markers in both panels, i was wondering if i could > > merge the two into a single flowSet with more channels. > > > > In details : > > > > - for panel A I have SSC, FSC, CD45, CD3, CD4, CD8, HLA-DR > > - for panel B I have SSC, FSC, CD45, CD3, CD5, CD19, CD16 > > > > I would like to obtain a single merged-panel with : SSC, FSC, CD3, CD45, > > CD4, CD8, CD5, CD19, CD16, HLA-DR > > > > I was thinking that the dataset is composed roughly of a matrix with for > > each leukocyte (event, =row) a value for all channels above (columns). So, > > maybe it would be possible to try to clusterise by pairs the rows of panel > > A and those of panel B on common values of SSC, FSC, CD45 and CD3. The > > result dataset would take the mean of the common channels and then the > > single values for CD4, CD5, CD8, CD16, CD19, HLA-DR. > > > > I would be glad to have your comment on this before starting. Maybe it has > > already been done in some package, or maybe one would have a comment to > > take into accoutn before i start ? > > > > Thanks in advance. > > Julien > > > > -- > > Envoy?? de mon ENIAC > > > > Julien Textoris, MD, PhD > > Laboratoire d'immunologie, > > UMR CNRS 7278, INSERM U1095 > > Facult?? de M??decine Timone, Marseille > > +33 (0)4 91 32 49 71 > > > > Service d'anesth??sie et de r??animation > > H??pital Nord, Marseille > > +33 (0)4 91 96 55 31 > -- Envoyé de mon ENIAC Julien Textoris, MD, PhD Laboratoire d'immunologie, UMR CNRS 7278, INSERM U1095 Faculté de Médecine Timone, Marseille +33 (0)4 91 32 49 71 Service d'anesthésie et de réanimation Hôpital Nord, Marseille +33 (0)4 91 96 55 31 [[alternative HTML version deleted]]
ADD REPLYlink written 6.7 years ago by TEXTORIS Julien160
Answer: Merging various panel for flow cytometry
0
gravatar for Jiang, Mike
6.7 years ago by
Jiang, Mike1.2k
(Private Address)
Jiang, Mike1.2k wrote:
Julien, I don't think you can merge these two panels by paring rows/cells across samples. You may have to stick to two individual flowSets to represent,analyze and visualize these two panels respectively. Once you've extracted the higher-level of population statistics (proportion, MFI,i.e.),you can merge/associate by patient info. You can use pData() method to read/set phenoData for flowSet (patient id, sample name,...). Let me know if you need more help regarding to the usage of these flow tools. Mike
ADD COMMENTlink written 6.7 years ago by Jiang, Mike1.2k
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