data() doesn't work for fcs files?
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AJC ▴ 10
@ajc-6830
Last seen 6.2 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.

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:

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 • 1.3k views
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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?

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Greg Finak ▴ 150
@greg-finak-4594
Last seen 3.3 years ago