Question

data() doesn't work for fcs files?

0

Entering edit mode

AJC ▴ 10

@ajc-6830

Last seen 9.2 years ago

United States

Hello bioconductor/R experts,

Just you all know, I'm new to bioconductor packages and bioinformatics (I only did basic R programming which were more plug and chug style as I entered code line by line) so I need your help.

So I was using flowCore for my data which was initially processed via flowJo.

> fcs = read.FCS("exported.FCS3.fcs")

so read.FCS file worked (with some warnings but I was told that those warning will be fixed when flowJo vX updates next time)

Now I'm trying to use data().

> data(fcs)
Warning message:
In data(fcs) : data set ‘fcs’ not found

How come it is not found? I set the right directory (using setwd() ) and I made sure my file was there. I checked ?data() and I'm wondering if it doesn't take fcs files. If that's the case, what procedures do I need to follow to be able to use data()?

summary() showed the summary of my data nicely so I don't know what's the problem with data(). I would like to get your assistance as soon as possible. Thank you in advance.

P.S. If anyone can explain the difference between fcs, FCS2, and FCS3 could you please explain those for me as well?

flowCore flowjo data • 2.2k views

ADD COMMENT • link updated 10.0 years ago by Greg Finak ▴ 150 • written 10.0 years ago by AJC ▴ 10

1

Entering edit mode

data() is used to load data sets that have been distributed with the packages you have installed, but apparently you want to load your own data in to R, and I think you have already done this with read.FCS(). What are you trying to accomplish when you use the data(fcs) command?

ADD REPLY • link 10.0 years ago Martin Morgan 25k

score 0 · Answer 1 · 2014-11-25

Following up on what Martin has said, read.FCS has already loaded your data into R. You don't need to call data(). As Martin said, that is used to load data sets that are distributed with packages. Your data is already available in the flowFrame object named fcs. What warnings were you getting from read.FCS, and why would they have anything to do with FlowJo vX? Did you export your FCS files from flowJo? Please have a look at the flowCore, flowVis, and flowWorkspace vignettes. They go into detail on how to analyze your flow data in R. You may also want to consider having a look at openCyto opencyto.org), a bioconductor framework for flow analysis. Regarding your other question, FCS 1.0, 2.0, and 3.0 are data standards for flow cytometry data files. See (http://isac-net.org/Resources-for-Cytometrists/Data-Standards/Data-File-Standards/Flow-Cytometry-Data-File-Format-Standards.aspx) Best, Greg