"relabeled" is created, but no files inside

[mleipold]

Hi,

How long should the creation of the new FCS files take?

I updated Mac R to v3.2.3, and was finally able to install cytofCore as instructed. I already had XQuartz installed. I'm running Yosemite 10.10.3. I even updated all the R packages after updating R itself (which solved a couple of my initial installation errors).

---

I am able to load cytofCore and run cytofCore.updatePanel(). XQuartz opens, and I'm asked to select my template file (FCS in my case), then the files to be relabeled. It's after I hit "OK" there, that I have problems.

I get a "relabeled" folder, but it's empty. The folder itself appears immediately after hitting "OK", but even 10+ minutes later, I have no new FCS files. Originally I was trying this with 6 files, but it happens even with 2 files.

I tried having my template FCS be in a separate folder from the ones to be relabeled. I tried updating XQuartz (I think it was 2.7.0, it's now 2.7.8 after update).

As far as I can tell, updatePanel thinks it's done. I get my ">" prompt back in the R window (rather than the flashing line while I'm selecting my template and other FCS files).

I did try using a different template file which had more parameters than the one to be relabeled. I did not get anything like this: "If a metal is not found, it will ask whether you want to include a placeholder column of zeros, or if you want to omit that channel from that file." Instead, it just generated another empty "relabeled" folder.

I don't know if this matters, but I'm trying this on Helios files.

-Mike

[zbjornson]

Hi Mike: One 10 mb file took several seconds for me. This sounds like a silent failure. Do you ever get a "Writing ....fcs" message? If you send your template file and one of your files to fix I can try debugging it. (You definitely need your template file not located in the folder containing FCS files to fix.)

[mleipold]

Hi Zach,

No, I never get any "Writing..." message.

Here are two files in question:
https://www.dropbox.com/sh/9o2ixt8bw9gdxie/AAAIO5ThHvBm34UOTgyrM-UJa?dl=0

885d5 ctrl: has 89Y channel but no marker label. Also has some extra channels, like 127I.
1512...: has 89Y channel with CD45 marker, has fewer channels (eg, 127I is removed).

I would like "885d5 ctrl" to be made to look like "1512..."(template). I tried it again this morning on these two files, and again, I got the formation of an empty "relabeled" folder, with no error messages or "Writing...fcs".

Thanks,
Mike

[bevbaq]

Hi all, I'm unfortunately running into the same issue of the empty relabeled folder. CytofCore ran fine and executed without any obvious issues. I currently only have 6 files I need to process and am not sure how next to proceed. Any help with this matter would be greatly appreciated!

Thanks, Bev

[zbjornson]

Sorry for the delay. Mike, it worked alright for me with your two files.

> cytofCore.updatePanel(templateFile="/home/zbbjornson/rlb/ab_01.fcs", fcsFolder="/home/zbbjornson/rlb/fix/")
Before /$P3N/Y89Di/$P3S/89Y/, after \$P3N\Y89Di\$P3S\89Y_CD45\.

I would expect R to print an error in this case, but, for other reasons, three days after you opened this issue I updated the updatePanel function to explicitly print an error if it can't find the template file. I also see one of your files has a space in the filename. Can you try removing the space in case that's what was breaking it?

@bevbaq any chance you have a space or special char in your filenames? Did you install before or after 13-Mar?

(Also note the syntax above where I'm specifying the templateFile and fcsFolder in the command requires the 13-Mar-2016 version. If you omit those, then you'll get the GUI as before.)

[bevbaq]

Hi Zach,

I’ve removed all the spaces in my file names, but still resulting in an empty unlabeled folder. I installed after March 13th.

Bev

[zbjornson]

@bevbaq any way you can share your files please?

[mleipold]

Hi Zach,

Should I reinstall the cytofCore to take in your "updatePanel" function update?

-Mike

[bevbaq]

Hi Zach,

https://www.dropbox.com/sh/uobreivrz0f36h3/AACokYdq1rZVUQ_YpWAYgizAa?dl=0

Best, Bev

[bevbaq]

Hi Zach,

Sorry I just realized that I was using non-fcs files for my analysis. Now
that I've got a relabeled folder with the panel updated, I've put them into
FlowJo. Though I'm seeing that I have >30,000 cells for each sample, I am
unable to see the events for any sample. Any thoughts?

Best, Bev

[zbjornson]

@mleipold yes, rerun install_github.

@bevbaq if you upload one of the relabeled files I can look. Some guesses are scaling, corrupt file...

[bevbaq]

https://www.dropbox.com/sh/uobreivrz0f36h3/AACokYdq1rZVUQ_YpWAYgizAa?dl=0

[zbjornson]

@bevbaq those all load and show events for me... and I actually see ~380k to 750k events per file...

[mleipold]

Hi Zach,

I reran install_github. It doesn't seem to have made any difference. I still don't get any error message, and I still get an empty relabeled folder.

I have attached screenshots of my folder hierarchy and GUI, in case I'm still not doing something right.

original files.png: I used 031016-Mike-Ichiro-UAB-151201079-AB_01.FCS as the template in a "templatefile" folder. I used "filetobechanged" as my target directory to be changed. It gave me an empty "relabeled" folder.

files without spaced.png: I used 031016-Mike-Ichiro-UAB-151201079-AB_01.FCS as the template in a "templatefile" folder. I used "filetobechanged-nospace" as my target directory to be changed; the target FCS had the space removed in the name. It gave me an empty "relabeled" folder.

empty relabeled folder.png: this screenshot is just meant to show where the "relabeled" folder wound up, in case it's not in the right place.

relabeled inside subfolders.png: I repeated the two attempts above, actually entering (rather than selecting) the target directory to be changed. The "relabeled" folders now appear inside the targeted directory folders, but are still empty.

Mike

[zbjornson]

@mleipold it looks like it didn't reinstall correctly from your screenshots. Can you try again, but run library("devtools") first:

library("devtools")
install_github("nolanlab/cytofCore")
library("cytofCore")

Then, it looks like (in at least some of your attempts) the template file couldn't be found for some reason -- wasn't selected, couldn't be read, other...

[mleipold]

@zbjornson

OK, I reran the installation:

R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

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Type 'q()' to quit R.

[R.app GUI 1.66 (7060) x86_64-apple-darwin13.4.0]

[History restored from /Users/michaelleipold/.Rapp.history]

library("devtools")
Warning message:
package ‘devtools’ was built under R version 3.2.5
install_github("nolanlab/cytofCore")
Skipping install for github remote, the SHA1 (cf2fe71) has not changed since last install.
Use force = TRUE to force installation
force = TRUE
install_github("nolanlab/cytofCore", force = TRUE)
Downloading GitHub repo nolanlab/cytofCore@master
from URL https://api.github.com/repos/nolanlab/cytofCore/zipball/master
Installing cytofCore
Skipping 1 unavailable package: flowCore
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save
--no-restore --quiet CMD INSTALL
'/private/var/folders/ln/_r_qkh8j1wz_wlrx0gw3mp100000gq/T/RtmpCczbsA/devtools142c4e27cece/nolanlab-cytofCore-cf2fe71'
--library='/Library/Frameworks/R.framework/Versions/3.2/Resources/library' --install-tests

• installing source package ‘cytofCore’ ...
  ** R
  ** inst
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** testing if installed package can be loaded
• DONE (cytofCore)

  library("cytofCore")
  Loading required package: flowCore
  cytofCore.updatePanel()

  ---

  It still gave me an empty "relabeled folder"

To be clear: I can still select the template FCS file in Step 1 of the process (ie, I click on an actual FCS file as the template; it appears).

For Step 2: "When choosing the folder, you must actually enter into that folder in the selection window before clicking OK." I'm entering into the folder containing the FCS file that I want to be relabeled, but I never see an FCS file in that folder.

Mike