FastBMD accepts tab-delimited text files (.txt) that contain a matrix of gene expression values as input. There is a standard format that needs to be followed - see the Data Upload section of the FAQs for more details.
If your organism is not among the list, you can still perform gene-level and transcriptome-level benchmark dose analysis. Please set this field and the ID field to "Annotation-free pipeline" to turn off ID conversion on your data.
If your ID type is not among the list, you can still perform gene-level and transcriptome-level benchmark dose analysis. Please set this field and the organism field to "Annotation-free pipeline" to turn off ID conversion on your data.
When multiple probes or transcripts are mapped to the same genes, you can choose to first summarize them to gene levels by using Mean or Median (microarray) or Sum (RNA-seq).
Upload your data as a tab-delimited text file (.txt). The maximum allowed file size is 100MB. The sample names must be in the first line, followed by the metadata labels. Each metadata starts with a new line beginning with "#CLASS:". A small example data with two metadata is shown below:
#NAME Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 Sample7 #CLASS:Dose 0 0 0.1 0.1 1.0 1.0 10.0 #CLASS:Sex M F F F M M F 100_g_at -3.06 -2.25 -1.15 -6.64 0.4 1.08 1.22 1000_at -1.36 -0.67 -0.17 -0.97 -2.32 -5.06 0.28 1002_f_at 1.61 -0.27 0.71 -0.62 0.14 0.11 1008_f_at 0.93 1.29 -0.23 -0.74 -2 -1.25 1.07
