nolanlab/bead-normalization

bead-based normalization of mass cytometry data

bead-normalization's Issues

unable to launch target application

Hello,

launching NormalizerR2013b_MacOSX.app as an admin user (OSX 10.11.5) succeeds, while doing the same as a non privileged user fails:

"Unable to launch target application. Exec of NormalizerR2013b_MacOSX failed".

Obviously a permissions issue, but applying the typical configuration measures still won't help.

Does the launch of that binary involves any symlinks or directory traversals which are not obvious?

Any hint would be great!

no

Normalization on data set with two panels

I ran a 9 donor, 9 day experiment on Helios with half samples stained with one panel and half with a separate panel, both with DVS beads. I used the bead-normalization tool to normalize the files all at once - is there any reason that this would be an issue? Should I stead normalize the samples with each panel separately? Thank you.

normalizer tries to read ._foobar.fcs files

such as when someone has transferred their data on an external hard drive that adds these hidden files

Normalizer Won't Open

Hi,

I just downloaded the stand-alone version of the normalizer on my iMac (running Sierra version 10.12.6) and installed the latest version of MATLAB Runtime for Mac (9.3) but get an error whenever I try to open the normalizer. I have attached a screenshot of the error.

Don't normalize "Event_length" channel

CyTOF2 uses "Event_length" instead of "Cell_length" and it shouldn't be normalized.

Ignore case of "FCS" extension

Think this is the line, but I'm not setup to compile this:

https://github.com/nolanlab/bead-normalization/blob/master/normalize_folder.m#L448

Came up on cytoforum this week.

random error while executing datenum

Hello,

on behalf of a colleague of mine:

1. The problem:
   "I have a data acquired with a CyTOF 1 and instrument control software 6.0.626 and I
   would like to normalize them with MATlab Normalizer R2013b_MacOSX. Some of
   the files work when I try to normalize them separatly but when I try to
   normalize them all together I will get an error.

Some of them give right away an error. In both cases the error is the same
as followed:

MATLAB:datenum:ConvertDateString
DATENUM failed.
datenumget_fcs_order111rderFilenames normalize_folder
line 11

We tried to rename the files but doesn't help.

Does anybody know what the error means and can help? Would be awesome."

2. Environment:
   The machine the normalizer is executed on:

• "nolanlab/bead-normalization" Normalizer v0.3
• installed from NormalizerR2013b_MacOSX.zip
• on OSX 10.9.

3. Guessing:
   It smells like being related to a Matlab classic as documented over here:
   http://www.mathworks.com/matlabcentral/newsreader/view_thread/287922#841230

... which then would turn this into a Matlab issue...

It looks like someone knowing the code of the normalizer could pinpoint the issue.

Would somebody please be so kind as to comment on this?

Best

using Rh103 as your DNA signal

Some CyTOF experiments use Rh103 as opposed to Ir191/193 to detect DNA. Currently, the normalizer throws an error that it does not find the DNA signal in this case. Could the normalizer be adapted to that Rh103 could be used as the DNA signal?

Concatenation fails - Sequence contains no elements

Hello,

we have following issue:

When having normalized files using

• Normalizer v0.3
• on Mac
• using the free Matlab-RE (NormalizerR2013b_MacOSX.zip)

concatenation of these normalized files will fail, when done via HELIOS (run on a 64bit Win7-PC).

Errormessage:

• ‘Sequence contains no elements’

Since it only occurs after having normalized the files:
Does someone have any idea what this is causing?
Is this known to be working this way usually or do we need to use another concatenation tool?

Best regards

Is there a way to include a sample in normalizer that is flagged as having "Bad Concatenation"?

I am using the normalizer and one of my samples was flagged as having "bad concatenation" and was skipped because "its time column is not monotonically increasing" - is there a way to fix this within the normalizer?

Calculating Bead Median question

Hi,

I am trying to port the Matlab bead Normalizer code to R.

The one thing I’m struggling with is the setNormalizationBaseline() function in normalize_folder.m. I understand that bead_means is a matrix of the median values for a the beadsbead across samples versus time.

What I’m unsure of (and this might just be my Matlab inexpertise) is how the median value is calculated across samples, since the number of timepoints is different for each sample. For example, is the median value for the first timepoint for Bead1(La139)Di in the example data calculated by just taking the first value for each of the four samples and finding the median?

In figure 2C in the paper, this appears to be the case, but I found the wording confusing because timepoint can refer to within-sample (as in timepoint at which a bead value was collected), or across samples (which correspond to different days).

Readout of normalisation results

I wanted to know whether there is a way of generating another readout of the normalisation results that appears when the normalisation is complete. I'm referring to the file that opens automatically and shows the comparison of median intensities of bead events before and after normalisation. I am a post-grad student using the tool and would like to include this figure in slides showing my methods, however I didn't save a copy of the readout. A .png file saves automatically but this is not of high quality. Is there a way of generating the report again without re-running the normalisation?

I have attached an image from the accompanying paper (Finck, R. et al. Cytom. A. 2013; 83(5): 483–494) to illustrate which readout I mean.
Thanks.

make error message useful when bead channel names don't match

e.g. (139Di) and (139Dd)

.exe no longer functions, "Error in mclFreeStackTrace"

just FYI, myself and others at my institution are having this error starting since at least over the weekend. App was working as early as last week. I realize users are getting pointed to the ParkerICI R platform, but would be dope if the simple executable could work again

Axis labels on MATlab normalizer

Hello,

We are running into a problem in which it seems like our image has a "zoom in" problem where we are unable to see the scaling of the Y axis. Please see image below. Is there a fix to this problem going forward?
Thank you!

Matlab Normalizer

Hi,

I normalized my fcs files using a same referral normalized fcs file for two independent batches. For one batch "before" and "after" graphs were generated but for the other batch there was no graphs generated in the "after" normalization plot.Not sure what is the issue? Any inputs would be greatly appreciated. Please contact me at [email protected]

Thank you,
Sangeeta