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March 10, 2015


How do I format my data for Batch Upload?


The Batch Upload process in GeneSifter is best suited for users that have data from multiple arrays in a single file, or users who want to upload data in a platform-generic way using NCBI RefSeq IDs, Affy probe IDs, or miRNAs.

  1. Data Format
  2. The following instructions detail how to format your data before uploading to GeneSifter.

    1. Data IDs - The first column "A" can accept one of the following: RefSeq IDs, Affy Probe IDs, or miRNAs. The column header should be left blank. See the blue section in Fig 1. where RefSeq values are used as the example.

    2. Gene Name - The second column "B" should be used for gene names. Like column A, column B's header should be left blank. Note that column B is optional and can be left blank. If you chose to leave it out the column mush be present, just with no values in it. See the green section in Fig 1. for an example.

    3. Data values - Column C should have your first experiment's data. The column header should be the Target name you want to use with Experiment One. See See the yellow section in Fig 1. for an example.

    4. Quality values - Column D should be used for quality information if you have it. If you do not, just assign every value to "1". The header should be the Condition name you want to use with Experimnet One. See the yellow section in Fig 1. for an example.

    5. Remaining Data - The approach outlined for Col C and D should be used for all remaining experiemnts that you wish to upload with this file. An example of this is shown in Figure 1 in shades of yellow.

    Figure 1 - "This image is a color coded generic array file in spreadsheet format. You can download this example file here". The instructions in the data format section details more information on how to format your data to fit this convention.

  3. File Upload:

    1. Login and select Batch Upload
    2. Select Batch Upload
    3. Name array and select file.
    4. Choose File and Upload
      Once your file has uploaded you can continue on and do analysis in GeneSifter.


    Q: Can I label House Keeping Genes?

    A: Yes, you can label House Keeping Genes by adding a "HKG" Column at position C. See example below.
    Labeling House Keeping Genes

    Q: After my data uploaded I saw a message that some of my data points failed to upload. For example "498 out of 500". What did I do wrong?

    A: The most common reason for failed data points is due to malformed data. Check your file for odd or non-English characters that might be causing interpretation problems. Make sure your numerical data are in the format 123456.78 as well. In other words, remove commas and use period to separate decimal places.

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