Arguments
EBPrelim
Output from the function EBTest().
FDR
Target FDR, defaut is 0.05.
FDRMethod
"hard" or "soft".
Giving a target FDR alpha, either hard threshold and soft
threshold may be used. If the hard threshold is preferred, DE transcripts are
defined as the the transcripts with PP(DE) greater than
(1-alpha). Using the hard threshold, any DE transcript in the list
has FDR
Method
"robust" or "classic".
Using the "robust" option, EBSeq is more robust to genes with outliers and
genes with extremely small variances.
Using the "classic" option, the results will be more comparable to those obtained
by using the GetPPMat() function from earlier version (
Threshold_FC
Threshold for the fold change (FC) statistics.
The default is 0.7. The FC statistics are calculated as follows.
First the posterior FC estimates are calculated using PostFC() function.
The FC statistics is defined as exp(-|log posterior FC|) and therefore is always less than
or equal to 1.
The default threshold was selected as the optimal threshold learned from our simulation studies. By setting the
threshold as 0.7, the expected FC for a DE transcript is less than 0.7
(or greater than 1/0.7=1.4).
User may specify their own threshold here. A higher (less conservative) threshold
may be used here when sample size is large. Our simulation results
indicated that when there are more than or equal to 5 samples in each condition,
a less conservative threshold will improve the power when the FDR is still well-controlled.
The parameter will be ignored if Method is set as "classic".
Threshold_FCRatio
Threshold for the fold change ratio (FCRatio) statistics.
The default is 0.3. The FCRatio statistics are calculated as follows.
First we get another revised fold change
statistic called Median-FC statistic for each transcript.
For each transcript, we calculate the median of
normalized expression values within each condition.
The MedianFC is defined as exp(-|log((C1Median+SmallNum)/(C2Median+SmallNum))|).
Note a small number is added to avoid Inf and NA. See SmallNum for more details.
The FCRatio is calculated as exp(-|log(FCstatistics/MedianFC)|).
Therefore it is always less than or equal to 1.
The default threshold was selected as the optimal threshold learned from our simulation studies.
By setting the threshold as 0.3, the FCRatio for a DE transcript is
expected to be larger than 0.3.
SmallNum
When calculating the FCRatio (or Median-FC), a small number is added for each transcript in each
condition to avoid Inf and NA. Default is 0.01.