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

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