datainput.md
In ideal: Interactive Differential Expression AnaLysis

ideal accepts only text files, either comma, semicolon, or tab-separated. This avoids proprietary formats such as Excel, which can also inadvertently convert your gene identifiers to dates or floating point numbers (SEPT2, see more here)
the delimiter used in the text file should be automatically guessed with a heuristic rule
for count data: features are in the rows, samples are stored in the columns
for the metadata: each row stores the relevant experimental variables of each sample
for the gene annotation: each row relates to a feature (i.e. a gene), with its id in the row names, and at least a column called gene_name, containing a more readable format (e.g. HGNC gene symbols)
it is important to have headers, as they are used in constructing the dds object and checking its validity: for example, the column names of the count matrix have to be identical to the row names of the sample metadata. This small constraint guarantees a higher degree of robustness for all the subsequent steps
if your data in stored in Excel sheets, export them to csv format (specify the correct separator accordingly when loading the data - you can always open them in a text editor to check)
general reminder: if you launch ideal directly from the terminal/RStudio IDE, you can pre-compute the objects, this can speed up