Along the lines of documentation, a human readable description of the steps used to create the odf in the header of the odf would be great for inevitable GEO submissions.
a) Filtering steps used to denote the gene as expressed (Exp in how many samples, etc)
b) Differential expression method used (voom (standard of other)/edgeR
c) Cutoff used for the gene list (logFC, FDR cutoff)
d) Versions of software
e) Using this method XXX genes were significantly upregulated / YYY downregulated.
Could also be exported part of an XLXS file with a README tab if you want to keep everything together.
Along the lines of documentation, a human readable description of the steps used to create the odf in the header of the odf would be great for inevitable GEO submissions. a) Filtering steps used to denote the gene as expressed (Exp in how many samples, etc) b) Differential expression method used (voom (standard of other)/edgeR c) Cutoff used for the gene list (logFC, FDR cutoff) d) Versions of software e) Using this method XXX genes were significantly upregulated / YYY downregulated.
Could also be exported part of an XLXS file with a README tab if you want to keep everything together.