Frequently Asked Questions (FAQs)
  1. Is the data that I uploaded kept confidential?
  2. What types of data does FastBMD accept?
  3. How many samples can I upload for an analysis?
  4. What is the minimum number of concentrations required for dose-response analysis?
  5. How to label a gene expression table?
  6. How to format a gene expression table?
  7. What if my microarray platform or organism is not supported?
  1. Is the data that I uploaded kept confidential?

    Yes. The data files you upload for analysis as well as any analysis results, are not downloaded or examined in any way by the administrators, unless required for system maintenance and troubleshooting. All files will be deleted automatically after 72 hours, and no archives or backups are kept. You are advised to download your results immediately after performing an analysis.

  2. What types of data does FastBMD accept?

    FastBMD accepts data from 13 species. The ID types supported for each species are given below:

    The data should be formatted in a matrix containing expression values (i.e. gene/probe intensities from microarray, counts from RNA-seq) saved as a tab delimited text file (.txt) with rows for features (genes/probes) and columns for samples. The tab delimited file can be generated from any spreadsheet program. More details are provided in the following sections.

  3. How many samples can I upload for an analysis?

    There is a 50MB limit for the uploaded data. For gene expression profiles with 20 000 genes, this corresponds to about 300 samples.

  4. What is the minimum number of concentrations required for dose-response analysis?

    FastBMD does not enforce a minimum number of concentrations, although it is recommended to have at least three in addition to the control samples.

  5. How to label a gene expression table?

    It is critical to properly label your data so that they can be recognized and compared. The following common IDs are supported:

    1. Gene ID: Entrez ID, Ensembl Gene ID, GenBank Accession ID, RefSeq ID, Ensembl Transcript ID, and official Gene Symbol
    2. Probe ID: popular microarray plotforms from Affymetrix, Agilent, Illumina;

    The gene expression data also should contain sample names in the first line. Each sample name should be unique. The class labels of experimental conditions should be in a new line beginning with "#CLASS". Multiple class labels can be indicated by adding a colon and its name (for example, "#CLASS:DOSE" and "#CLASS:SEX").

  6. How to format a gene expression table?

    Here is a good tutorial on how to generate tab delimited text files from the Excel Spreadsheet program. When you open your data using any text editor (for example, WordPad), it should look like the following:

    • Sample name, one class label (one missing value)
              #NAME	Sample1	Sample2	Sample3	Sample4	Sampl5	Sampl6	Sample7	Sample8
              #CLASS	0	0	0.1	0.1	1.0	1.0	10.0	10.0
              Gene1	-3.06	-2.25	-1.15	-6.64	0.4	1.08	1.22	1.02
              Gene2	-1.36	-0.67	-0.17	-0.97	-2.32	-5.06	0.28	1.32
              Gene3	1.61	-0.27	0.71	-0.62	0.14		0.11	0.98
              Gene4	0.93	1.29	-0.23	-0.74	-2	-1.25	1.07	1.27
                                              
    • Sample name, two class labels (cancer and sex)
              #NAME           Sample1	Sample2	Sample3	Sample4	Sampl5	Sampl6	Sample7	Sample8
              #CLASS:DOSE	0	0	0.1	0.1	1.0	1.0	10.0	10.0
              #CLASS:SEX	F	F	M	M	F	M	F	M
              Gene1           -3.06	-2.25	-1.15	-6.64	0.4	1.08	1.22	1.02
              Gene2           -1.36	-0.67	-0.17	-0.97	-2.32	-5.06	0.28	1.32
              Gene3           1.61	-0.27	0.71	-0.62	0.14		0.11	0.98
              Gene4           0.93	1.29	-0.23	-0.74	-2	-1.25	1.07	1.27
                                              
  7. What if my microarray platform or organism is not supported?

    You have three options:

    1. Select "Annotation-free pipeline" for the organism and ID type. You can perform all analyses except for pathway-level BMD analysis.
    2. Use the microarray annotation file to annotate probes to one of the common gene IDs that are supported (entrez, refseq, ensemble, etc).
    3. It is possible to add support for other model organisms/platforms based on user requests. Feel free to send us your suggestions. Note, this could take a while depending on the available time.