Hi all I want to find the DE for miRNAs. I have a factor type and multiple values for that factor. I want to calculate the DE in a design in which I can compare one value to the mean of the other values. It is possible in edgeR if you give a coefficient to your group but I don't know how to simulate it in DESeq. Thanks in advance Maryam [[alternative HTML version deleted]]

> I want to find the DE for miRNAs. I have a factor type and multiple values > for that factor. I want to calculate the DE in a design in which I can > compare one value to the mean of the other values. It is possible in edgeR > if you give a coefficient to your group but I don't know how to simulate it > in DESeq. To compare one factor level against the average of all other factor levels, the easiest might be to redefine the factor to have only two levels (the level of interest and "other"), and test for this. As you would then have a higher dispersion in the "other" level, you may also want to use the "per-condition" dispersion method. For DESeq2, you could construct a design matrix with "sum" contrasts, using your level of interest as the last one, and this should also give the desired test. However, are you sure you must compare to the average of the other conditions, rather than compare to a control condition? After all, even if only one condition is very different to the others, you may find not only this condition to differ significantly from the averages of the others, but also all other conditions, too, because the outlying condition changes the average you compare against. S