Answers.Body: <p>I found my answer in <a href="https://lists.purdue.edu/pipermail/cytometry/2012-June/043612.html" rel="nofollow noreferrer">an old mailing list</a>. Credit to Josef Spidlen who authored the mail.</p>
  <p><em>Short answer</em>: both parameters are proprietary keywords from the BD FACSDiva software for storing scaling values.</p>
  <p><em>Long answer</em> from the mailing list:</p>
  <blockquote>
  <p><strong>PnBS</strong> Indicates the automatically set Biexponential scale value for Instrument  Parameter (-1 indicates an invalid scale value). When
  importing an FCS  file, if the FCS file has valid Biexponential
  scales, they should be  applied to the data. If the FCS file doesn't
  have valid biexponential  scales then the scales are calculated from
  the entire data. If  biexponential scales exist, then if AUTOBS is
  set, the PnBS values are  used and applied to the data. If AUTOBS is
  not set, the PnMS values are  used and applied to the data. The
  information represented by this keyword becomes part of a Tube's
  attributes, and does not appear in the Tube's list of keywords. It can
  be viewed in the Biexponential inspector' when the auto scaling option
  is selected.</p>
  <p><strong>PnMS</strong> Indicates the manually set Biexponential scale value for Instrument  Parameter (-1 indicates an invalid scale value). When
  importing an FCS  file, if the FCS file has valid Biexponential
  scales, they should be  applied to the data. If the FCS file doesn't
  have valid biexponential  scales then the scales are calculated from
  the entire data. If  biexponential scales exist, then if AUTOBS is
  set, the PnBS values are  used and applied to the data. If AUTOBS is
  not set, the PnMS values are  used and applied to the data. The
  information represented by this keyword becomes part of a Tube's
  attributes, and does not appear in the Tube's list of keywords. It can
  be viewed in the Biexponential inspector' when the manual scaling
  option  is selected.</p>
  </blockquote>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-07-28T09:33:56.327Z
Answers.LastActivityDate: 2022-07-28T09:33:56.327Z
Answers.UserDisplayName: RoB
Body: <p>I'm using the <a href="http://www.bioconductor.org/packages/release/bioc/html/flowCore.html" rel="nofollow noreferrer">flowCore</a> packages to analyze cytometry data, and I am trying to understand all the parameters stored in the FCS file.
  I've figured out most of the elements, but despite a thorough search I haven't been able to find documentation on some of the parameters.</p>
  <p>For each channel, there are 9 associated parameters. Here's P1 and its associated values from one of my files :</p>
  <ul>
  <li><code>$P1N</code>    FSC-A</li>
  <li><code>$P1R</code>    262144</li>
  <li><code>$P1B</code>    32</li>
  <li><code>$P1E</code>    0,0</li>
  <li><code>$P1V</code>    225</li>
  <li><code>$P1G</code>    1</li>
  <li><code>$P1DISPLAY</code>  LIN</li>
  <li><code>$P1BS</code>   0</li>
  <li><code>$P1MS</code>   0</li>
  </ul>
  <p>I've figured out the following from various sources (notably the FCS data standards, given <a href="https://isac-net.org/page/Data-Standards" rel="nofollow noreferrer">here</a>) or from the fields themselves:</p>
  <ul>
  <li><code>$PnN</code> Short name for parameter n.</li>
  <li><code>$PnR</code> Range for parameter number n.</li>
  <li><code>$PnB</code> Number of bits reserved for parameter number n.</li>
  <li><code>$PnE</code> Amplification type for parameter n.</li>
  <li><code>$PnV</code> Detector voltage for parameter n.</li>
  <li><code>$PnG</code> Amplifier gain used for acquisition of parameter n.</li>
  <li><code>$PnDISPLAY</code>  the transformation to apply when displaying the data (e.g. LIN, LOG)</li>
  </ul>
  <p>However, these 2 don't appear in the file standard description, and flowCore does not have documentation on the parameters either.</p>
  <ul>
  <li><code>$PnBS</code></li>
  <li><code>$PnMS</code></li>
  </ul>
  <p>I've seen <code>$PnBS</code> set at -1, 0, 48, 57, 54, 52 or 25 for various channels in my data, while <code>$PnMS</code> always seems to be at 0.</p>
  <p>Does someone know what it is, or where to look for a definition?
  If that helps, my FCS files were generated through BD FACSDiva Software Version 9.0.1.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-26T12:54:09.083Z
Comments.Text: As this is a package from Bioconductor I would recommend to ask on their site: support.bioconductor.org. Probably you'll get a helpful answer, but it would be nice to know where do you find these parameters
Comments.UserDisplayName: llrs
Tags: <r><flow-cytometry>
Title: What do "PnBS" and "PnMS" mean in FCS flowCore parameters?
ThreadText: # What do "PnBS" and "PnMS" mean in FCS flowCore parameters?
  
  (Asked by: username_0 on 2022-07-26)
  
  I'm using the [flowCore](http://www.bioconductor.org/packages/release/bioc/html/flowCore.html) packages to analyze cytometry data, and I am trying to understand all the parameters stored in the FCS file.
  I've figured out most of the elements, but despite a thorough search I haven't been able to find documentation on some of the parameters.
  
  For each channel, there are 9 associated parameters. Here's P1 and its associated values from one of my files :
  
  * `$P1N` FSC-A
  * `$P1R` 262144
  * `$P1B` 32
  * `$P1E` 0,0
  * `$P1V` 225
  * `$P1G` 1
  * `$P1DISPLAY` LIN
  * `$P1BS` 0
  * `$P1MS` 0
  
  I've figured out the following from various sources (notably the FCS data standards, given [here](https://isac-net.org/page/Data-Standards)) or from the fields themselves:
  
  * `$PnN` Short name for parameter n.
  * `$PnR` Range for parameter number n.
  * `$PnB` Number of bits reserved for parameter number n.
  * `$PnE` Amplification type for parameter n.
  * `$PnV` Detector voltage for parameter n.
  * `$PnG` Amplifier gain used for acquisition of parameter n.
  * `$PnDISPLAY` the transformation to apply when displaying the data (e.g. LIN, LOG)
  
  However, these 2 don't appear in the file standard description, and flowCore does not have documentation on the parameters either.
  
  * `$PnBS`
  * `$PnMS`
  
  I've seen `$PnBS` set at -1, 0, 48, 57, 54, 52 or 25 for various channels in my data, while `$PnMS` always seems to be at 0.
  
  Does someone know what it is, or where to look for a definition?
  If that helps, my FCS files were generated through BD FACSDiva Software Version 9.0.1.
  
  **Tags:** r, flow-cytometry
  
  > **Comments:**
  > **username_1**: As this is a package from Bioconductor I would recommend to ask on their site: support.bioconductor.org. Probably you'll get a helpful answer, but it would be nice to know where do you find these parameters  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2022-07-28. Score: 0 | Accepted answer
  
  I found my answer in [an old mailing list](https://lists.purdue.edu/pipermail/cytometry/2012-June/043612.html). Credit to Josef Spidlen who authored the mail.
  
  *Short answer*: both parameters are proprietary keywords from the BD FACSDiva software for storing scaling values.
  
  *Long answer* from the mailing list:
  
  > **PnBS** Indicates the automatically set Biexponential scale value for Instrument Parameter (-1 indicates an invalid scale value). When
  > importing an FCS file, if the FCS file has valid Biexponential
  > scales, they should be applied to the data. If the FCS file doesn't
  > have valid biexponential scales then the scales are calculated from
  > the entire data. If biexponential scales exist, then if AUTOBS is
  > set, the PnBS values are used and applied to the data. If AUTOBS is
  > not set, the PnMS values are used and applied to the data. The
  > information represented by this keyword becomes part of a Tube's
  > attributes, and does not appear in the Tube's list of keywords. It can
  > be viewed in the Biexponential inspector' when the auto scaling option
  > is selected.
  >
  > **PnMS** Indicates the manually set Biexponential scale value for Instrument Parameter (-1 indicates an invalid scale value). When
  > importing an FCS file, if the FCS file has valid Biexponential
  > scales, they should be applied to the data. If the FCS file doesn't
  > have valid biexponential scales then the scales are calculated from
  > the entire data. If biexponential scales exist, then if AUTOBS is
  > set, the PnBS values are used and applied to the data. If AUTOBS is
  > not set, the PnMS values are used and applied to the data. The
  > information represented by this keyword becomes part of a Tube's
  > attributes, and does not appear in the Tube's list of keywords. It can
  > be viewed in the Biexponential inspector' when the manual scaling
  > option is selected.
  
  
  ---
  
  