Issue with flowAI and flow_auto_qc
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@vinkotosevski-14950
Last seen 22 months ago

Dear all,

I have recently tried to run flowautoqc of flowAI package and was getting the following error:

fs_qced <- flow_auto_qc(fs, remove_from = "FR_FS")
Quality control for the file: export_CD45+
Error in R[j] <- R[j - 1] - dj : replacement has length zero
In addition: Warning message:
In cffilter(x) : # of observations < 5

I am not finding any specific reference to this type of problem in the context of flowAI and have tried also inputting flowFrame(s) and FCS file path(s). The same files are amenable to flowAI's flow_iQC interactive method, which suggests there's nothing wrong with FCS files themselves (ran few other sanity checks as well). I am not sure what the problem is. In the past flowAI worked without issues and much hassle around it. Can someone help?

I am using flowAi 1.14 on R 3.6.1. with Bioconductor 3.9 in place.

Thanks, Vinko

flowAI flow_auto_qc QC flow cytometry • 550 views
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gianni • 0
@gianni-9478
Last seen 3.2 years ago

Dear Vinko,

The error you get should be about the fact that you have a low number of events in your FCS file, maybe less than 1000. Is that true?

I should improve the way flowAI handles files with low number of events. For now just disregard them or use flow_iQC.

Best,

Gianni

On Nov 3, 2019, at 11:59 AM, vinko.tosevski [bioc] <noreply@bioconductor.org<a rel="nofollow" href="mailto:noreply@bioconductor.org">noreply@bioconductor.org> wrote:

Activity on a post you are following on support.bioconductor.orghttps://support.bioconductor.org/

User vinko.tosevskihttps://support.bioconductor.org/u/14950/ wrote Question: Issue with flowAI and flowautoqchttps://support.bioconductor.org/p/126060/:

Dear all,

I have recently tried to run flowautoqc of flowAI package and was getting the following error:

fsqced <- flowautoqc(fs, removefrom = "FRFS") Quality control for the file: exportCD45+ Error in R[j] <- R[j - 1] - dj : replacement has length zero In addition: Warning message: In cffilter(x) : # of observations < 5

I am not finding any specific reference to this type of problem in the context of flowAI and have tried also inputting flowFrame(s) and FCS file path(s). The same files are amenable to flowAI's flow_iQC interactive method, which suggests there's nothing wrong with FCS files themselves (ran few other sanity checks as well). I am not sure what the problem is. In the past flowAI worked without issues and much hassle around it. Can someone help?

I am using flowAi 1.14 on R 3.6.1. with Bioconductor 3.9 in place.

Thanks, Vinko

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Hi Gianni,

Thanks for the fast reply. I don't think it's about low number of events. I have 12 files in the flowSet and each FCS file has around 100'000 cells. What else could it be?

Vinko

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I am not sure why you are having this problem then. Would you be able to share with me one of the files?

On Nov 3, 2019, at 3:52 PM, vinko.tosevski [bioc] <noreply@bioconductor.org<a rel="nofollow" href="mailto:noreply@bioconductor.org">noreply@bioconductor.org> wrote:

Activity on a post you are following on support.bioconductor.orghttps://support.bioconductor.org/

User vinko.tosevskihttps://support.bioconductor.org/u/14950/ wrote Comment: Issue with flowAI and flowautoqchttps://support.bioconductor.org/p/126060/#126067:

Hi Gianni,

Thanks for the fast reply. I don't think it's about low number of events. I have 12 files in the flowSet and each FCS file has around 100'000 cells. What else could it be?

Vinko

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Dear @gianni. I've have the same problem... could you solve it? Thanks for your help.

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I still need a file to test the issue. If you have one, please send it to me.

On Mar 9, 2020, at 7:10 PM, jgarces [bioc] <noreply@bioconductor.org<a rel="nofollow" href="mailto:noreply@bioconductor.org">noreply@bioconductor.org> wrote:

Activity on a post you are following on support.bioconductor.orghttps://support.bioconductor.org/

User jgarceshttps://support.bioconductor.org/u/20286/ wrote Comment: Issue with flowAI and flowautoqchttps://support.bioconductor.org/p/126060/#128924:

Dear @gianni. I've have the same problem... could you solve it? Thanks for your help.

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I'm working with a LMD file (not the classical FCS format), I also asked you in GitHub... maybe the problem could be here? But yes, indeed, I'll send you an example if you tell me your email, please. Or another server to upload it? Thanks

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Hi,

I uploaded a new version which should be able to also work with LMD files.

Best, Gianni

On Mar 10, 2020, at 4:29 PM, jgarces [bioc] <noreply@bioconductor.org<a rel="nofollow" href="mailto:noreply@bioconductor.org">noreply@bioconductor.org> wrote:

Activity on a post you are following on support.bioconductor.orghttps://support.bioconductor.org/

User jgarceshttps://support.bioconductor.org/u/20286/ wrote Comment: Issue with flowAI and flowautoqchttps://support.bioconductor.org/p/126060/#128940:

I'm working with a LMD file (not the classical FCS format), I also asked you in GitHubhttps://github.com/SamGG/flowAI/issues/1... maybe the problem could be here? But yes, indeed, I'll send you an example if you tell me your email, please. Or another server to upload it? Thanks

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