Merge pull request #169 from nf-core/affy_docs

Affy docs

CHANGELOG.md

@@ -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`
 

docs/usage.md

@@ -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