Version 1.1

• A checkbox has been added to filter out samples where QC.status=QC.fail. This option is for GCT files ONLY. If the QC.status column does not exist and the box is checked, a warning message is printed and analysis will proceed using all samples.
• A warning message appears when attempting to log-transform a dataset that contains negative values (i.e., a dataset that has already been log-transformed). In this case, log-transformation will not occur to prevent downstream analysis errors.
• An error message appears when a column label has only one sample assigned to it, and analysis will not proceed. ProTIGY requires all column labels have more than one sample assigned to them. When this error appears, the user must either remove that sample from the file, or use another column for statistical testing and/or group-wise normalization.
• A checkbox has been added to indicate the data are intensity data rather than ratios. When the box is checked, normalization methods, filtering methods, and statistical testing will be automatically filtered to only methods appropriate for intensity data. Further, the missing value rate will be capped at 99%, as the statistical analysis can fail when the missing value rate is 100%.
• For the moderated two-sample t-test and the moderated F test, eBayes(trend=true) is used for intensity data. This option is more stable for intensity data, but does require the capped missing value rate of 99%. eBayes(trend=FALSE) continues to be used for ratios.
• Help text has been edited for non-GCT files to clarify that NA must be used for missing sample annotations. Further, a sample can be excluded in a non-GCT file by leaving the Experiment and Group annotations as NA.