These are the instructions for formatting your microarray data so that we can easily upload it into and host it on Microbes Online.
We need the following information:
- The NCBI taxonomy id of the organism.
- The microarray platform used (Ex: Affymetric, Nimblegen, etc...)
- The name of the researcher and/or institution that performed these experiments
- The email of the person to contact if we have any questions about the data
- If this data is to be kept private until publication, please include a list of email addresses that should be authorized to see the data on MicrobesOnline
- An experiment list file : click here to see an example
This file REQUIRES the following header columns (Group_ID, Set_ID, Stress, Organism, Treatment Time (min), Control time (min), tFactor, and cFactor).
Please note the Group_ID and Set_ID. For entries with the same experimental condition (Stress), the Group_ID needs to be the same.
This allows the grouping of different microarray experiments into the same series for analysis.
The Set_ID is a member of a group, but they differ typically in time points.
The Group_ID and Set_ID are combined with an underscore "_" to make the column headers in the data files below.
Please use an underscore as dashes "-" and ":" cause excel to interpret the information as dates or times.
The "t" in tFactor indicates treatment and "c" in cFactor stands for control.
- A normalized log ratio or log level data file : click here to see an example
As stated above the column headers correspond to the Group_ID concatenated with an underscore and the Set_ID.
The row headers need to be the RefSeq accessions for the genes that the value corresponds to.
The values in this file should all be normalized as a Log2 ratio or level.
- A confidence value data file - click here to see an example
(NOTE: This confidence file is optional.). If you have the data we will upload it.
When sending the data to us please indicate what the confidence value corresponds to (e.g. p-value, z-score, FDR) and which method was used produce it.
This file is the same format as the log file.
Please note if you include a confidence file the column headers and row headers
must match exactly (in order, case, length, etc) between the confidence file and the log file.
If you have any questions, please email us