RSeqFlow-OlivePollen2: RSeqFlow1_results_2023-02-09_16.03.33.zip
Manuel Gonzalo Claros · Figshare · 2023
Compressed file of the RSeqFlow folder that contains the report and results of olive pollen tube growth. Files with extension .tsv contain tab separated values. Taking into account that {DATETIME} = 2023-02-09_16.03.33 (date and time when it was executed), the following files can be found, in alphabetical order: • Report.html: The complete report explaining the analysis, including figures, analysis rationale, bibliography and explanation of each saved file. • AllGenes_allContrast_TREAT-P-0.1_FC-1.2_{DATETIME}.tsv: Average expression, coefficient (LogFC), t statistic, P value, adjusted P value, F statistic, and DEG result for all genes in each of the contrasts using the treat method and the P and FC indicated in the filename. • AllGenes_allContrast_eB_P-0.1_FC-1.2_{DATETIME}.tsv: Average expression, coefficient (LogFC), t statistic, Pvalue, adjusted P value, F statistic, and DEG result for all genes in each of the contrasts using the eBayes method and the P and FC indicated in the filename. • AllGenes_{CONTRAST}_TREAT_{DATETIME}.tsv: LogFC, average expression, P value, and adjusted P value, for all genes in the contrast indicated in {CONTRAST} using the treat method. • BestCorrelations_{METHOD}_{CLUSTER}-{DATETIME}.tsv: Correlation (r), P value, and adjusted P value for the pair of genes (Item1 and Item2) in each cluster {CLUSTER} obtained with the algorithm {METHOD}. • ClustersCTF-{DATETIME}.tsv: Averaged CTFs of the DEGs present in any cluster, indicating the number of the cluster and method where it appears. • CTFnormalisedCPMs-{DATETIME}.tsv: Normalised CPMs for each gene (rows) in each sample replicate (columns) using the CTF algorithm. • DEGs_{CONTRAST}_TREAT_P-0.1_FC-1.2_{DATETIME}.tsv: LogFC, average expression, t statistic, P value, and adjusted P value, for all DEGs (rows) in the contrast indicated in {CONTRAST} using the treat method and the Pand FC indicated in the filename. • DEGs_{CONTRAST}_eB_P-0.1_FC-1.2_{DATETIME}.tsv: LogFC, average expression, t statistic, P value, adjusted P value, and B statistic for all DEGs (rows) in the contrast indicated in {CONTRAST} using the eBayes method and the P and FC indicated in the filename. • filteredData-{DATETIME}.tsv: Raw counts in all sample replicates (columns) for genes (rows) that presented a reliable expression. • List_of_clusters-{DATETIME}.Rds: R object containing all the information about clusters obtained with the three clustering methods AHC, k-means and MBC. It must be read with the R function readRDS() to inspect or use its contents. • normHomoscedCPM-{DATETIME}.tsv: TMM-normalised and homeoscedastic counts of reliable genes (rows) in all sample replicates (columns). • OutstandingGenes-{DATETIME}.tsv: Highly linked genes in the different clusters that can be considered hub genes. • TMMnormalisedCounts-{DATETIME}.tsv: Normalised counts for each gene (rows) in each sample replicate (columns) using the TMM algorithm. • TMMnormalisedCPMs-{DATETIME}.tsv: Normalised CPMs for each gene (rows) in each sample replicate (columns) using the TMM algorithm. • ubiquitousDEGs_{DATETIME}.tsv: List of genes that are DEGs in all the contrast performed in the analysis, including if it is up-regulated (1) or down-regulated (-1) en each contrast.