GitLab

script for the differential abundance analysis of mass spec data with limma; based on the dge_workflow/limma/dge_limma.R script

revised code for plotting of lfq intensities and added density plot for all unique and ambiguous entries per sample; cosmetics

fixed bug in CON__ REV__ and STANDARD__ removal: now all corresponding unique entries and all biased entries which only contain any of these features are removed; added export of protein information and filtered for one fasta_header per protein_id only; cosmetics

added peptide intensities of STANDARDs (boxplot and heatmap); corrected data plotting with scale_y_log10 and now use intensities+1 to make sure we do not lose the zero intensities; added export of top10 LFQs per sample

fixed bugs: now only unique CON, REV and STANDARD entries are removed from the intensities matrix; old_protein_ids are now included in the right_join when summarizing sample information; file name of exported sample information is now corrected

added the following: summary of STANDARD raw and LFQ intensities, summary of samples per input file, sorting of protein IDs before merging the tables and reporting of the number of changed protein IDs orders, boxplot of LFQ intensities per sample, reporting of renaming scheme, some general documentation; cosmetics

changed the following: if no gene_info file is provided and the first colname of the count matrix is != 'ensembl_gene_id', the corresponding first column will be reported as geneInfo and geneDescs

added "protein_ids" (ID of ms_data_prep.R output) as firstColName option when checking the input count matrix

started with ms_workflow specific scripts; first entry: ms_data_prep.R to prepare MaxQuant proteinGroups.txt files for differential abundance analysis with limma

changed the independent filtering method in the DESeq2 results() function from the default to independent hypothesis weighting (IHW)