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How to best use peacoQC() in Spectre workflow? #149
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I would use I'm not familiar with how PeacoQC works, but if it takes FCS files, then the output of |
Thanks @ghar1821 for your response! When you get a chance, would you mind helping me address 4 questions below?
Thank you for your help!
|
Answers to your questions:
Rather than writing out the flowJo's transformed value out as csv file then converting it to fcs file using Spectre, is it not possible to just get flowJo to export those transformed values as fcs files? |
Thanks @ghar1821 and @tomashhurst. QUESTION 2. Performing
And, if I run
If I run write.files() nested in the
Lastly, if thus run simply If I set the
In conclusion, would you say running Although now, the file name of the outputted FCS will just be I am ok with this, but the issue is when I then used these exported FCS files in
QUESTION 3. |
@ghar1821 commenting at RGLab/flowCore#243 |
Pasting the reply I initially wrote for RGLab/flowCore#243 here:
The NULL showed in the console is because
No this doesn't make sense. Don't do it.
This is the expected behaviour. If
Yes.
What about using FileName as
I think you will still get the error regardless of whether you use 1 or 4 FCS files. I have a feeling this is because the data.table does not store the instrument range - though I'm not 100% as I don't normally use FCS file. Now, whether this matters for downstream analysis really depends on what your subsequent steps are. I'll see if I can find the time write up a guide on how to use peacoQC to do preprocessing, and Spectre for subsequent downstream analysis. |
From @denvercal1234GitHub reply originally posted at RGLab/flowCore#243:
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The issue was identified due to file naming of PE markers across wells. See RGLab/flowCore#243 Solution = change the marker names before exporting the data from cytometer into FlowJo and subsequent R packages. Thank you again @ghar1821 for taking the time to look into the issue. And, I look forward to reading the tutorials whenever you get a chance to do it. Keeping it open because unsure if Givanna's tag for documentation would disappear if closed. |
Hi there,
I am following the tutorial (https://immunedynamics.io/spectre/simple-discovery/#6_Annotate_clusters).
I input the channel values of my data into Spectre. Then, I do
write.files()
as below to export these channel values as FCS without doing any transformation or clustering, because I now want to use these FlowJo-transformed FCS files in peacoQC package before putting back the QC-files to Spectre.Is it better to use CSV-to-FCS script instead of this
write.files()
?Thank you for your help.
Related: sydneycytometry/CSV-to-FCS#6
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