GeneLab_Data_Processing
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nasa
## Description The following error occurred when rendering `Affymetrix.qmd`: ``` Error in oligo::read.celfiles(df_local_paths$`Local Paths`, sampleNames = df_local_paths$`Sample Name`) : The annotation package, pd.mogene.1.0.st.v1, could not be loaded. ``` [`read.celfiles()`](https://www.rdocumentation.org/packages/oligo/versions/1.36.1/topics/read.celfiles) automatically...
## Description No issues when using Nextflow v.22.10.0.5826, but after updating to Nextflow v.23.10.1.5891, the following error arose in `AGILE1CH` / `PROCESS_AFFYMETRIX` processes from `quarto render` command: ``` Could not...
Generate protocol from template (similar to `GENERATE_PROTOCOL` in Affymetrix pipeline)
Parse logs from tools (or MultiQC report) to generate metrics CSV (each row is a sample, each column is a metric)
MultiQC reports are currently generated separately for each tool. Perhaps combine into one or two reports (e.g., FASTQC/Trim Galore! into one report where metrics are reported at read-level, STAR/RSeQC/RSEM in...
changed WF name, fixed some documentation, and removed the Estimate Host Reads WF from PR @bnovak32 @asaravia-butler
## Description Density plots currently scale down legend size depending on number of samples: https://github.com/nasa/GeneLab_Data_Processing/blob/90d6bb5d6a20d817fa17ac5cb0763d4f8f75966b/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/workflow_code/bin/Affymetrix.qmd#L248 But plot may sometimes still be covered by legend when sample names are long. ##...
## Description For one dataset with AFFY HTA 2 0 probes, the probe IDs have `.hg.1` suffix whereas biomaRt data uses `.hg` suffix, causing the data not to be able...
Currently, MA plots for raw data may be plotted differently depending on the type of data: https://github.com/nasa/GeneLab_Data_Processing/blob/90d6bb5d6a20d817fa17ac5cb0763d4f8f75966b/Microarray/Affymetrix/Workflow_Documentation/NF_MAAffymetrix/workflow_code/bin/Affymetrix.qmd#L295-L316 Track different classes of data and how to plot the MA plots for...