The updated DNAmAge calculator currently takes 24-48 hours to generate the results. Resubmissions are not necessary except when Error messages have been sent.
Necessary Fields for Sample Annotation File
When submitting your sample annotation CSV file, please make sure it includes the following columns/fields:
Sample_Name - the values in this column of the sample sheet should match the values in the first row of the methylation data (if submitting a CSV of beta values rather than IDAT files)
Tissue - typically this value is: Whole Blood, PBMCs, Saliva, Liver, Kidney, Cerebellum, etc.
Age - chronological age as a number in years
Sex - 0 is male, 1 is female, or NA for not available. Should only be numeric values.
If submitting IDAT files, the following field is necessary:
Basename - This is the unique identifier for the IDAT file, such as 207182140036_R01C01, 207182140036_R02C01, etc.
If obtaining analysis upgrades, the following fields are necessary:
Group - this is typically "Treatment" vs. "Control", or "Diseased" vs. "Control" (necessary for Group & EWAS Analysis)
VolCode - this is a unique patient or study volunteer identifier such as "HLTH5", "HLTH6", etc. (necessary for Individual Reports)
CollectionDate - this is the date the sample was collected in the following format (YYYY-MM-DD) (necessary for Individual Reports)
Note the spelling and capitalization of each field. Make sure to submit a comma delimited file (which is generated with Excel or Google Sheets) rather than a semicolon- or tab-delimited file.
Methylation Data
When submitting your methylation data, you can now submit either IDAT files or beta values. Make sure to upload all the probe names (cg numbers) mentioned in the updated file below.
List of CpG Probes Necessary for Full Results: datMiniAnnotation4_fixed.csv
We have found that noob normalization (preprocessNoob in minfi) or quantile normalization (preprocessQuantile in minfi) often lead to the highest accuracy. Above all, avoid missing values when it comes to preprocessing your data.
If the corresponding probes are missing in your data set, fill up the row with “NA” (which indicates that the values are not available). As with the sample sheet, ensure that a comma-delimited file is submitted rather than a semicolon- or tab-delimited file.
For additional reference, a tutorial is available in the TutorialOnlineCalculator.doc (Note: However, this tutorial is currently still based on the OLD DNAmAge calculator site).
Why are my results not available, or why are their missing values for some biomarkers?
a) The DNAmAge calculator currently takes 24-48 hours to return results.
It is not necessary to resubmit projects unless an Error message has been sent.
b) Make sure that your DNA methylation data file contains all the necessary probes.
List of CpG Probes Necessary for Full Results: datMiniAnnotation4_fixed.csv
c) Make sure that you upload numeric data (missing values should be coded as NA and not as null or NULL).
Carefully look at your methylation data matrix before you upload it. The first column should contain CpG identifiers. The remaining columns should only contain numeric values. If a column (sample) only contains missing values, remove it from the file. If need be, run the following R code before you upload the data. for (i in 2:dim(dat0)[[2]] ) { dat0[,i]=as.numeric(as.character(dat0[,i])) }
d) Project status will also be available in your web account, and it should reflect either Pending, Running, Error, or Done.
Resubmissions are only necessary when an Error status message has been delivered. However, please feel free to reach out to us at anytime (info@clockfoundation.org).