In the first part of the panel the A
vs. M
plots per sample are depicted.
The values are defined as follows
where $I_i$ and $I_j$ are transformed values. In the case of raw,
normalized, or batch corrected the values are log2
-transformed
prior to calculating A
and M
if there are no negative values in the
data sets. In case of transformed or imputed
the values are taken as they are (N.B. when the transformation
method is set to none the values are not log2
-transformed).
The imputed data set can only be selected if there are
missing values (NA
s) in the raw data set.
The values for $I_i$ are taken from the sample $i$. For $I_j$, the feature-wise
means are calculated from the values of the group $j$ of samples specified
by the drop-down menu group. The sample for calculating $I_i$ is
excluded from the group $j$. The group can be set to "all"
(i.e. all samples except sample $i$ are used to calculate
$I_j$) or any other column in colData(se)
. For any group except "all"
the
group is taken to which the sample $i$ belongs to and the sample $i$ is
excluded from the feature-wise calculation.
The MA values for all samples are by default displayed facet-wise. The MA plot can be set to specific samples by changing the selected value in the input menu plot.
The underlying data set can be selected by the drop-down menu (Data set for the MA plot).
In the second part of the tab, the Hoeffding's D statistic values are
visualized for the different data sets raw, normalized,
batch corrected, transformed, and imputed. The imputed
values are only displayed if there are missing values (NA
s) in
the raw data set.
D
is a measure of the distance between F(A, M)
and G(A)H(M)
, where
F(A, M)
is the joint cumulative distribution function (CDF) of
A
and M
, and G
and H
are marginal CDFs.
The higher the value of D
, the more dependent are A
and M
.
For reasons of computational efficiency, a subset of 5000 features
will be randomly sampled from the SummarizedExperiment
object.
In case there are less than 5000 features, all features of the
SummarizedExperiment
are taken.
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