From 63e5f030a975a83c8d3f49ef62e0309295620a79 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 16 Oct 2023 13:50:18 +0100 Subject: [PATCH 1/4] Clarify sample sheet preparation in docs for Affy --- assets/samplesheet.csv | 3 --- docs/usage.md | 18 ++++++++++++++++++ 2 files changed, 18 insertions(+), 3 deletions(-) delete mode 100644 assets/samplesheet.csv diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv deleted file mode 100644 index 5f653ab7..00000000 --- a/assets/samplesheet.csv +++ /dev/null @@ -1,3 +0,0 @@ -sample,fastq_1,fastq_2 -SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz -SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz, diff --git a/docs/usage.md b/docs/usage.md index 32059219..e753640b 100644 --- a/docs/usage.md +++ b/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 From ebcde7854d060989d862093dfd11b9d4cd0c9a87 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 16 Oct 2023 13:53:45 +0100 Subject: [PATCH 2/4] Update CHANGELOG --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 932dc3c6..c192ab99 100644 --- a/CHANGELOG.md +++ b/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` From 2793b196ac855c51f82c431491d278a8a945905f Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 16 Oct 2023 13:57:37 +0100 Subject: [PATCH 3/4] Just poking CI --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c192ab99..03903eab 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,7 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#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 [@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 ) +- [[#119](https://github.com/nf-core/differentialabundance/issues/119)] - Document sample sheet for Affy arrays ([@pinin4fjords](https://github.com/pinin4fjords), review by) ### `Fixed` From 689a5a894043ac5f469d3c0d5ac7cac2302d6aa1 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 16 Oct 2023 13:58:26 +0100 Subject: [PATCH 4/4] remove extra space --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 03903eab..5fa705ec 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,7 +15,7 @@ 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 [@WackerO](https://github.com/WackerO)) +- [[#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`