RSeqFlow-OlivePollen2: RSeqFlow1_results_2023-02-09_16.03.33.zip

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