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ParkerICI / premessa

R package for pre-processing of mass and flow cytometry data
GNU General Public License v3.0
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Error messeage in step "normalizer_GUI" #23

Closed LilyJNJ closed 5 years ago

LilyJNJ commented 6 years ago

Hi,

I have 20 .FCS files, when I use "normalizer_GUI" to normalize them one by one, 10 files can have output "xxx_normalized.fcs", but the other 10 got an error messeage:

Warning: Error in solve.default: system is computationally singular: reciprocal condition number = 1.00251e-19 93: solve.default 91: mahalanobis 90: get_mahalanobis_distance_from_beads 88: FUN 87: lapply 86: premessa::normalize_folder 73: observeEventHandler [C:\Users\ywang535\Documents\R\R-3.4.4\library\premessa\normalizer_shinyGUI/server.R#266] 2: shiny::runApp 1: normalizer_GUI

Setting is just default, as this: image Screenshot of error in R is this: image

Can you help me with this? Thank you!

pfgherardini commented 6 years ago

Hi

Yes I am aware of what's causing this problem. Can you please send me one of the FCS files that causes the problem so that I can reproduce it on my computer and verify that I have a fix? You can use a Box or Dropbox link to share the file.

Thanks

Federico

LilyJNJ commented 5 years ago

Hi Federico,

Sorry for the late reply, just back from a business trip. Here is the Dropbox link to a FCS file. https://www.dropbox.com/s/86hlndcav592w6q/JCLD_20180429_000909_01.FCS?dl=0 Thank you~

Best, Lily

发件人: Pier Federico Gherardini notifications@github.com 发送时间: 2018年11月9日 6:31 收件人: ParkerICI/premessa 抄送: LilyJNJ; Author 主题: Re: [ParkerICI/premessa] Error messeage in step "normalizer_GUI" (#23)

Hi

Yes I am aware of what's causing this problem. Can you please send me one of the FCS files that causes the problem so that I can reproduce it on my computer and verify that I have a fix? You can use a Box or Dropbox link to share the file.

Thanks

Federico

― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ParkerICI/premessa/issues/23#issuecomment-437180212, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AqmCoK634f_NSUTe-GUzHFYJNyEJhG5Gks5utLDRgaJpZM4YF4RP.

pfgherardini commented 5 years ago

Are you sure you are gating the beads properly? I only get that error if I leave the gates as default (which is obvioulsy incorrect), but everything works fine once the gates are adjusted

LilyJNJ commented 5 years ago

Hi, I'm very new to Cytof so I don't know how to gate properly... So maybe it's due to my false gating. Thank you for your help.

发件人: Pier Federico Gherardini notifications@github.com 发送时间: 2018年11月29日 2:54 收件人: ParkerICI/premessa 抄送: LilyJNJ; Author 主题: Re: [ParkerICI/premessa] Error messeage in step "normalizer_GUI" (#23)

Are you sure you are gating the beads properly? I only get that error if I leave the gates as default (which is obvioulsy incorrect), but everything works fine once the gates are adjusted

― You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ParkerICI/premessa/issues/23#issuecomment-442562416, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AqmCoJNrKbdN2-9hbUKPLmCHYKJI_ixQks5uztvSgaJpZM4YF4RP.

pfgherardini commented 5 years ago

No problem. You have to use the plot to gate the bead population for each file, which will normally be a population in the lower right corner of the plot. See for example here