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Affy docs #169

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Oct 16, 2023
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Affy docs #169

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63e5f03
Clarify sample sheet preparation in docs for Affy
pinin4fjords Oct 16, 2023
ebcde78
Update CHANGELOG
pinin4fjords Oct 16, 2023
2793b19
Just poking CI
pinin4fjords Oct 16, 2023
689a5a8
remove extra space
pinin4fjords Oct 16, 2023
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -15,7 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#137](https://github.com/nf-core/differentialabundance/pull/137)] - Add `--sizefactors_from_controls` and `--gene_id_col` for DESeq2 module to modules.config ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#145](https://github.com/nf-core/differentialabundance/pull/145)] - Template update for nf-core/tools v2.9 ([@nf-core-bot](https://github.com/nf-core-bot), review by [@pinin4fjords](https://github.com/pinin4fjords), [@WackerO](https://github.com/WackerO))
- [[#147](https://github.com/nf-core/differentialabundance/pull/147)] - Add Maxquant analysis module ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#166](https://github.com/nf-core/differentialabundance/issues/166)] - Output a parameter-resolved R Markdown document, as well as rendered HTML ([@pinin4fjords](https://github.com/pinin4fjords), review by )
- [[#166](https://github.com/nf-core/differentialabundance/issues/166)] - Output a parameter-resolved R Markdown document, as well as rendered HTML ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
- [[#119](https://github.com/nf-core/differentialabundance/issues/119)] - Document sample sheet for Affy arrays ([@pinin4fjords](https://github.com/pinin4fjords), review by)

### `Fixed`

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3 changes: 0 additions & 3 deletions assets/samplesheet.csv
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18 changes: 18 additions & 0 deletions docs/usage.md
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Expand Up @@ -39,6 +39,24 @@ TREATED_REP3,AEG588A2_S1_L004_R1_001.fastq.gz,AEG588A2_S1_L004_R2_001.fastq.gz,t

The file can be tab or comma separated.

### Affymetrix arrays

Abundances for Affy arrays are provided in CEL files within an archive. When creating sample sheets for Affy arrays, it's crucial to include a column that specifies which file corresponds to each sample. This file column is essential for linking each sample to its corresponding data file, as shown in the example below:

```
"file","id","name","patient","phenotype"
"GSM1229341_Gudjohnsson_001_6690_PP.CEL.gz","GSM1229341","p6690_PP","6690","lesional"
"GSM1229342_Gudjohnsson_002_6690_PN.CEL.gz","GSM1229342","p6690_PN","6690","uninvolved"
"GSM1229343_Gudjohnsson_003_7450_PN.CEL.gz","GSM1229343","p7450_PN","7450","uninvolved"
"GSM1229344_Gudjohnsson_004_7450_PP.CEL.gz","GSM1229344","p7450_PP","7450","lesional"
"GSM1229345_Gudjohnsson_005_7912_PP.CEL.gz","GSM1229345","p7912_PP","7912","lesional"
"GSM1229346_Gudjohnsson_006_7912_PN.CEL.gz","GSM1229346","p7912_PN","7912","uninvolved"
"GSM1229347_Gudjohnsson_007_8470_PP.CEL.gz","GSM1229347","p8470_PP","6690","lesional"
"GSM1229348_Gudjohnsson_008_8470_PN.CEL.gz","GSM1229348","p8470_PN","6690","uninvolved"
```

The "file" column in this example is used to specify the data file associated with each sample, which is essential for data analysis and interpretation.

## Abundance values

### RNA-seq and similar
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