writing out FCS files then reading them back in
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Jiang, Mike ★ 1.3k
@jiang-mike-4886
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On Fri, Jul 24, 2015 at 3:30 PM, Mike <wjiang2@fhcrc.org> wrote:

It works for me. Since you are trying to use flowCore 3.14.7 which is published for BioC3.1 + R 3.2,  it would be best if you could simply upgrade your R.

 


On 07/24/2015 11:46 AM, Arnaud Colantonio wrote:

Mike,

By using a different delimiter the problem was solved.  However I am running into another issue now.  When trying to load FCS files using the flowCore 1.35.7  I am getting the following error:

Error in ls(object@frames, all.names = TRUE) : 

  could not find symbol "sorted" in environment of the generic function

I have never seen this before. I am still running on R 3.1.2 with Biobase 2.26.0 and BiocGenerics 0.12.1.  Are there any depending libraries that would be causing this problem that would also need to be updated

Arnaud



On Thu, Jul 23, 2015 at 1:55 PM, Mike <wjiang2@fhcrc.org> wrote:
Try to pick a different 'delimiter' (e.g. delimiter = '|') instead of default '\'  when you 'write.FCS ' to see if this helps.

 


On 07/23/2015 10:40 AM, Arnaud Colantonio wrote:

Hi Mike,

I am attempting to do so preprocessing on FCS files for a collaborator.  Essentially what I am looking to do is gate on subsets of cells and files individual FCS files from each of these subsets.  I am starting small by trying to use the write.FCS function but I am running into problems.

Below is a sample of the reading and writing.  I haven't even started to gate the data yet.

 

for(i in 1:length(files)) {

  fSet <- read.FCS(file.path(base.dir,files[i]))

  write.FCS(fSet,file.path(base.dir,gsub(".fcs","_refnorm.fcs",files[i])))                                    

}

 

When i try to read the files back in I get:

Error: Empty keyword name detected!If it is due to the double delimiters in keyword value, please set emptyValue to FALSE and try again!

Setting emptyValue to FALSE seems to work but this only worked after I updates to flowCore 1.35.7.

The situation decribed above will work for fcs files from a fortessa but the situation is even stranger when I try with FCS files from CytOF.  In that case the above code results in file sizes that are 3x smaller and no way to read them even if I set emptyValue to FALSE.

Any suggestions?

Thanks,

Arnaud

flowcore flow cytometry • 843 views
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