Multiplexting output - #823
Open
mschwoer wants to merge 3 commits into
Open
Conversation
GeorgWa
requested changes
Jul 20, 2026
GeorgWa
left a comment
GeorgWa
left a comment
Collaborator
There was a problem hiding this comment.
The current approach creates separate files per channel. If we analyse 10 samples with 3 channels this creates the slightly akward situation that we have 3 matrix files with 10 samples each. I think the more natural way is to have a single matrix file with 3x10=30 columns/samples (like DIANN).
--- # Conversation that produced these changes --- ## User prompt "The current approach creates separate files per channel. If we analyse 10 samples with 3 channels this creates the slightly akward situation that we have 3 matrix files with 10 samples each. I think the more natural way is to have a single matrix file with 3x10=30 columns/samples (like DIANN)." ## Clarifying round 1 Q: How should the per-(run, channel) columns be named? - run_0.ch4 - run_0_ch4 - run_0.4 <-- chosen: "change it to run_0.channel_CHANNELNAME" ## Clarifying round 2 Q: precursor.matrix / peptide.matrix rows are already channel-specific (multiplexing replaces label mods, so mod_seq_charge_hash differs per channel). pg.matrix rows are shared across channels. How should the merged files be shaped? - 30 cols everywhere <-- chosen - 30 cols pg, channel col below - 10 cols + channel col Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Add per-channel output for multiplexing