Problem reading files on FlowCore
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Sancho, Jose ▴ 80
@sancho-jose-3937
Last seen 7.3 years ago
I am new to FlowCore, and I am trying to get the demo files,as described on Flow Cytometry data analysis using Bioconductor- A typical work flow, and having difficulties. I type the instruction flowData <-read.flowSet(path = "C:\Documents and Settings\sanjo05\My Documents\BIOCONDUCTOR SOFTWARE", phenodata = "annotation.txt", + transformation = FALSE). I get the following error message Error: unexpected '=' in "flowData <-read.flowSet(path = "C:\Documents and Settings\sanjo05\My Documents\BIOCONDUCTOR SOFTWARE", "annotation.txt", + transformation =" What am I doing wrong? Thanks Jose Sancho Genzyme Corporation Flow Cytometry Core Facility [[alternative HTML version deleted]]
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Chao-Jen Wong ▴ 580
@chao-jen-wong-3603
Last seen 7.0 years ago
USA/Seattle/Fred Hutchinson Cancer Reseā€¦
Hi Jose, May I ask why there is a "+" sign before the transformation argument? -C.J. Sancho, Jose wrote: > I am new to FlowCore, and I am trying to get the demo files,as described > on Flow Cytometry data analysis using Bioconductor- A typical work flow, > and having difficulties. > > > > I type the instruction flowData <-read.flowSet(path = "C:\Documents and > Settings\sanjo05\My Documents\BIOCONDUCTOR SOFTWARE", phenodata = > "annotation.txt", + transformation = FALSE). > > > > I get the following error message Error: unexpected '=' in "flowData > <-read.flowSet(path = "C:\Documents and Settings\sanjo05\My > Documents\BIOCONDUCTOR SOFTWARE", "annotation.txt", + transformation =" > > > > What am I doing wrong? > > > > Thanks > > > > Jose Sancho > > > > Genzyme Corporation > > Flow Cytometry Core Facility > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M2-B876 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org
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I am afraid I do not know. I am following the instructions as set on Flow cytometry data analysis using Bioconductor - A typical work flow. Nishant Gopalakrishnan July 23, 2009 And I can't load the fcs files. -----Original Message----- From: Chao-Jen Wong [mailto:cwon2@fhcrc.org] Sent: Wednesday, February 17, 2010 6:04 PM To: Sancho, Jose Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Problem reading files on FlowCore Hi Jose, May I ask why there is a "+" sign before the transformation argument? -C.J. Sancho, Jose wrote: > I am new to FlowCore, and I am trying to get the demo files,as described > on Flow Cytometry data analysis using Bioconductor- A typical work flow, > and having difficulties. > > > > I type the instruction flowData <-read.flowSet(path = "C:\Documents and > Settings\sanjo05\My Documents\BIOCONDUCTOR SOFTWARE", phenodata = > "annotation.txt", + transformation = FALSE). > > > > I get the following error message Error: unexpected '=' in "flowData > <-read.flowSet(path = "C:\Documents and Settings\sanjo05\My > Documents\BIOCONDUCTOR SOFTWARE", "annotation.txt", + transformation =" > > > > What am I doing wrong? > > > > Thanks > > > > Jose Sancho > > > > Genzyme Corporation > > Flow Cytometry Core Facility > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M2-B876 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2@fhcrc.org [[alternative HTML version deleted]]
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Hi Sancho, Each line of code in a vignette starts with a ">" . Parts of a code chunk that does not fit into a single line and get carried over to the next line get a "+" at the beginning of the line. Additionally, the phenoData argument is case sensitive. (You have used phenodata) It would be a good idea to get familiar with the syntax of R before attempting to go through work flows. Nishant Sancho, Jose wrote: > I am afraid I do not know. I am following the instructions as set on > Flow cytometry data analysis using Bioconductor - A typical work flow. > > Nishant Gopalakrishnan > > July 23, 2009 > > > > And I can't load the fcs files. > > > > -----Original Message----- > From: Chao-Jen Wong [mailto:cwon2 at fhcrc.org] > Sent: Wednesday, February 17, 2010 6:04 PM > To: Sancho, Jose > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Problem reading files on FlowCore > > > > Hi Jose, > > > > May I ask why there is a "+" sign before the transformation argument? > > > > -C.J. > > > > Sancho, Jose wrote: > > >> I am new to FlowCore, and I am trying to get the demo files,as >> > described > > >> on Flow Cytometry data analysis using Bioconductor- A typical work >> > flow, > > >> and having difficulties. >> > > > > >> >> > > > > >> I type the instruction flowData <-read.flowSet(path = "C:\Documents >> > and > > >> Settings\sanjo05\My Documents\BIOCONDUCTOR SOFTWARE", phenodata = >> > > >> "annotation.txt", + transformation = FALSE). >> > > > > >> >> > > > > >> I get the following error message Error: unexpected '=' in "flowData >> > > >> <-read.flowSet(path = "C:\Documents and Settings\sanjo05\My >> > > >> Documents\BIOCONDUCTOR SOFTWARE", "annotation.txt", + transformation >> > =" > > > > >> >> > > > > >> What am I doing wrong? >> > > > > >> >> > > > > >> Thanks >> > > > > >> >> > > > > >> Jose Sancho >> > > > > >> >> > > > > >> Genzyme Corporation >> > > > > >> Flow Cytometry Core Facility >> > > > > > > >> [[alternative HTML version deleted]] >> > > > > >> _______________________________________________ >> > > >> Bioconductor mailing list >> > > >> Bioconductor at stat.math.ethz.ch >> > > >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > >> Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor > > >> >> > > > > > >
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Eliminate the "+" sign on your command. The "+" sign on Nishant's workflow document (and all the bioconductor vignette) indicates that the compound expression or arguments are continuing. It is automatically added by R. When you program in R, you don't need to manually write "+". Chao-Jen Sancho, Jose wrote: > > I am afraid I do not know. I am following the instructions as set on > Flow cytometry data analysis using Bioconductor - A typical work flow. > > Nishant Gopalakrishnan > > July 23, 2009 > > > > And I can?t load the fcs files. > > > > -----Original Message----- > From: Chao-Jen Wong [mailto:cwon2 at fhcrc.org] > Sent: Wednesday, February 17, 2010 6:04 PM > To: Sancho, Jose > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Problem reading files on FlowCore > > > > Hi Jose, > > > > May I ask why there is a "+" sign before the transformation argument? > > > > -C.J. > > > > Sancho, Jose wrote: > > > I am new to FlowCore, and I am trying to get the demo files,as described > > > on Flow Cytometry data analysis using Bioconductor- A typical work flow, > > > and having difficulties. > > > > > > > > > > > > I type the instruction flowData <-read.flowSet(path = "C:\Documents and > > > Settings\sanjo05\My Documents\BIOCONDUCTOR SOFTWARE", phenodata = > > > "annotation.txt", + transformation = FALSE). > > > > > > > > > > > > I get the following error message Error: unexpected '=' in "flowData > > > <-read.flowSet(path = "C:\Documents and Settings\sanjo05\My > > > Documents\BIOCONDUCTOR SOFTWARE", "annotation.txt", + transformation =" > > > > > > > > > > > > What am I doing wrong? > > > > > > > > > > > > Thanks > > > > > > > > > > > > Jose Sancho > > > > > > > > > > > > Genzyme Corporation > > > > > > Flow Cytometry Core Facility > > > > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > -- > > Chao-Jen Wong > > Program in Computational Biology > > Division of Public Health Sciences > > Fred Hutchinson Cancer Research Center > > 1100 Fairview Avenue N., M2-B876 > > PO Box 19024 > > Seattle, WA 98109 > > 206.667.4485 > > cwon2 at fhcrc.org > > > -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M2-B876 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org
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Thank you, Chao-Jen and Nishant for your answers. I am not really familiar with R, I just read a couple of papers regarding several software packages for Flow Cytometry analysis and I decided to give it a go, not as easy as it looks. Can you point me to the right source to familiarize with Flowcore? Once again, thanks. Jose Sancho Flow Cytometry Core Facility. Genzyme Corp. -----Original Message----- From: Chao-Jen Wong [mailto:cwon2@fhcrc.org] Sent: Thursday, February 18, 2010 2:43 PM To: Sancho, Jose Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Problem reading files on FlowCore Eliminate the "+" sign on your command. The "+" sign on Nishant's workflow document (and all the bioconductor vignette) indicates that the compound expression or arguments are continuing. It is automatically added by R. When you program in R, you don't need to manually write "+". Chao-Jen Sancho, Jose wrote: > > I am afraid I do not know. I am following the instructions as set on > Flow cytometry data analysis using Bioconductor - A typical work flow. > > Nishant Gopalakrishnan > > July 23, 2009 > > > > And I can't load the fcs files. > > > > -----Original Message----- > From: Chao-Jen Wong [mailto:cwon2 at fhcrc.org] > Sent: Wednesday, February 17, 2010 6:04 PM > To: Sancho, Jose > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Problem reading files on FlowCore > > > > Hi Jose, > > > > May I ask why there is a "+" sign before the transformation argument? > > > > -C.J. > > > > Sancho, Jose wrote: > > > I am new to FlowCore, and I am trying to get the demo files,as described > > > on Flow Cytometry data analysis using Bioconductor- A typical work flow, > > > and having difficulties. > > > > > > > > > > > > I type the instruction flowData <-read.flowSet(path = "C:\Documents and > > > Settings\sanjo05\My Documents\BIOCONDUCTOR SOFTWARE", phenodata = > > > "annotation.txt", + transformation = FALSE). > > > > > > > > > > > > I get the following error message Error: unexpected '=' in "flowData > > > <-read.flowSet(path = "C:\Documents and Settings\sanjo05\My > > > Documents\BIOCONDUCTOR SOFTWARE", "annotation.txt", + transformation =" > > > > > > > > > > > > What am I doing wrong? > > > > > > > > > > > > Thanks > > > > > > > > > > > > Jose Sancho > > > > > > > > > > > > Genzyme Corporation > > > > > > Flow Cytometry Core Facility > > > > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > > -- > > Chao-Jen Wong > > Program in Computational Biology > > Division of Public Health Sciences > > Fred Hutchinson Cancer Research Center > > 1100 Fairview Avenue N., M2-B876 > > PO Box 19024 > > Seattle, WA 98109 > > 206.667.4485 > > cwon2 at fhcrc.org > > > -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M2-B876 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org
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Hi, Jose, As Nishant has said, I think it is a good idea to get familiar with the basic syntax of R. You can go to CRAN's website, http://cran.r-project.org/manuals.html, and download the tutorial, "An introduction of R". Throughout this document, you will get familiar with R data structure, objects, functions and data manipulation. The vignette in the flowCore package provides details of functionalities provided by flowCore. It is a must-read document when you use Bioconductor's flow cytometry packages. To open the vignetter on your R console, you can do the following: > library(flowCore) > browseVignette("flowCore") R will open a browser in which you can find the vignette and the corresponding R chucks of the vignette. The functionalities provided by the flowStats packages are very useful for flow data analysis as well. Note that you'd better install the newest version of R is you want to use flowStats, especially for data normalization. Alternatively, you can try to use the iFlow package that provides a graphical user interface allowing you to explore your flow data. (An R-dev version is required to install iFlow.) Once you get familiar with flowCore, the flowClust and flowMerge packages are very useful if you wan to find clusters of cell populations. Let us know if you have any further questions. We will have a workshop at the cyto 2010 conference in Seattle in May. Authors of the Bioconductor flow packages will give presentation and teach people how to use the flow packages. You are welcome if you are interested. Chao-Jen Sancho, Jose wrote: > Thank you, Chao-Jen and Nishant for your answers. > > I am not really familiar with R, I just read a couple of papers > regarding several software packages for Flow Cytometry analysis and I > decided to give it a go, not as easy as it looks. > Can you point me to the right source to familiarize with Flowcore? > > Once again, thanks. > > Jose Sancho > Flow Cytometry Core Facility. > Genzyme Corp. > -----Original Message----- > From: Chao-Jen Wong [mailto:cwon2 at fhcrc.org] > Sent: Thursday, February 18, 2010 2:43 PM > To: Sancho, Jose > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Problem reading files on FlowCore > > Eliminate the "+" sign on your command. The "+" sign on Nishant's > workflow document (and all the bioconductor vignette) indicates that the > compound expression or arguments are continuing. It is automatically > added by R. When you program in R, you don't need to manually write > "+". > > Chao-Jen > > Sancho, Jose wrote: > >> I am afraid I do not know. I am following the instructions as set on >> Flow cytometry data analysis using Bioconductor - A typical work flow. >> >> Nishant Gopalakrishnan >> >> July 23, 2009 >> >> >> >> And I can't load the fcs files. >> >> >> >> -----Original Message----- >> From: Chao-Jen Wong [mailto:cwon2 at fhcrc.org] >> Sent: Wednesday, February 17, 2010 6:04 PM >> To: Sancho, Jose >> Cc: bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] Problem reading files on FlowCore >> >> >> >> Hi Jose, >> >> >> >> May I ask why there is a "+" sign before the transformation argument? >> >> >> >> -C.J. >> >> >> >> Sancho, Jose wrote: >> >> >>> I am new to FlowCore, and I am trying to get the demo files,as >>> > described > >>> on Flow Cytometry data analysis using Bioconductor- A typical work >>> > flow, > >>> and having difficulties. >>> >>> I type the instruction flowData <-read.flowSet(path = "C:\Documents >>> > and > >>> Settings\sanjo05\My Documents\BIOCONDUCTOR SOFTWARE", phenodata = >>> >>> "annotation.txt", + transformation = FALSE). >>> >>> I get the following error message Error: unexpected '=' in "flowData >>> >>> <-read.flowSet(path = "C:\Documents and Settings\sanjo05\My >>> >>> Documents\BIOCONDUCTOR SOFTWARE", "annotation.txt", + transformation >>> > =" > >>> What am I doing wrong? >>> >>> Thanks >>> >>> Jose Sancho >>> >>> Genzyme Corporation >>> >>> Flow Cytometry Core Facility >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> >>> Bioconductor mailing list >>> >>> Bioconductor at stat.math.ethz.ch >>> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >>> Search the archives: >>> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >>> >>> >> >> >> >> >> -- >> >> Chao-Jen Wong >> >> Program in Computational Biology >> >> Division of Public Health Sciences >> >> Fred Hutchinson Cancer Research Center >> >> 1100 Fairview Avenue N., M2-B876 >> >> PO Box 19024 >> >> Seattle, WA 98109 >> >> 206.667.4485 >> >> cwon2 at fhcrc.org >> >> >> >> > > > -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M2-B876 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org
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