Closed ginnyintifa closed 1 year ago
For the second point, although it's redundant, keeping this gives users a little bit more flexibility for customizing the plot.
For the first point, I think they are for different purposes. [sample ID]_1 and [sample ID]_2 are technical replicates. The replicate column, however, is initially designed for bioreplicates as we have in the FragPipe manifest.
But it's actually confusing, for example, this is FragPipe manifest from ccRCC discovery DIA data: dia_manifest (1).fp-manifest.txt The experiment column is [Condition]_[sample num], and the replicate column here becomes more like technical replicates.
Updated in https://github.com/MonashProteomics/FragPipe-Analyst/commit/d17fbf9cdd388c8ae284599b64b19a3b5feb4913..
Now the combined_annotation.txt will looks like this | plex | channel | label | condition | replicate |
---|---|---|---|---|---|
3 | 126 | CPT0148080004 | Tumor | 1 | |
3 | 127N | CPT0148100003 | Normal | 1 | |
3 | 127C | CPT0083100003 | Tumor | 1 | |
3 | 128N | CPT0083140003 | Normal | 1 | |
3 | 128C | CPT0118160003 | Tumor | 1 | |
3 | 129N | CPT0118180003 | Normal | 1 | |
3 | 129C | CPT0105510003 | Tumor | 1 | |
3 | 130N | CPT0105550003 | Normal | 1 | |
3 | 130C | TumorOnlyIR03 | |||
3 | 131N | pool03 | pool | 3 | |
7 | 126 | CPT0109680004 | Tumor | 1 | |
7 | 127N | CPT0109700003 | Normal | 1 | |
7 | 127C | CPT0105940003 | Tumor | 1 | |
7 | 128N | CPT0105980003 | Normal | 1 | |
7 | 128C | CPT0090170004 | Tumor | 1 | |
7 | 129N | CPT0090200003 | Normal | 1 | |
7 | 129C | CPT0105330003 | Tumor | 1 | |
7 | 130N | CPT0105370004 | Normal | 1 | |
7 | 130C | CPT0148080004 | Tumor | 2 | |
7 | 131N | pool07 | pool | 7 |
Looking good! And do users need to change column names in the report now?
That's correct. Please let me know if you find any issue. Thanks for the contribution!
@ginnyintifa I would like re-open this. Actually, FragPipe doesn't allow users to have the same label for different samples anymore. Therefore, the user needs to indicate _1, _2 in the label column, and the shared prefix before _1, _2 is used to differentiate samples from different patients.
@ginnyintifa I would like re-open this. Actually, FragPipe doesn't allow users to have the same label for different samples anymore. Therefore, the user needs to indicate _1, _2 in the label column, and the shared prefix before _1, _2 is used to differentiate samples from different patients.
Really? in TMT workflow, duplicated labels in the same plex is not allowed. But if there are 2 name labels in different plexes, it is allowed right? But this would cause duplicates seen in TMT-I report.
Yes, but what I am talking about is which should be the standard way annotating samples. I still keep the logic for handling duplicate labels, but probably we should use _
In the TMT workflow, in the combined_annotative.tsv.
Some columns are redundant.
1 Replicate. We are not allowing user to have duplicated sample IDs i.e. label column. so the replicate isn't helpful.every row would have value 1 in this column. I don't know if this column would be involved in any calculation in the functionalities.
2 experiment/plex I think we can just keep one of them, preferrably experiment.