Detect differentially expressed genes (DEGs) in a standard ExpressionSet
object.
1 2 3 
ExpressionSet 
a standard PhyloExpressionSet or DivergenceExpressionSet object. 
nrep 
either a numeric value specifying the constant number of replicates per stage or a numeric vector specifying the variable number of replicates for each stage position. 
method 
method to detect differentially expressed genes. 
lib.size 
the library sizes to equalize library sizes by quantiletoquantile normalization (see 
p.adjust.method 
p value correction method. 
comparison 
a character string specifying whether genes having foldchange or pvalues
below, above, or below AND above (both) the 
alpha 
a numeric value specifying the cutoff value above which Genes fulfilling the corresponding foldchange, logfoldchange, or pvalue should be retained and returned by 
filter.method 
a method how to 
n 
a numeric value for 
stage.names 
a character vector specifying the new names of collapsed stages. 
All methods to perform dection of differentially expressed genes assume that your input
dataset has been normalized before passing it to DiffGenes. For RNASeq data
DiffGenes assumes that the libraries have been normalized to have the same size, i.e.,
to have the same expected column sum under the null hypothesis. If this isn't the case
please run equalizeLibSizes
before calling DiffGenes.
Available methods for the detection of differentially expressed genes:
method = "foldchange"
: ratio of replicate geometric means between developmental stages.
Here, the DiffGenes functions assumes that absolute expression levels are stored in your input ExpresisonSet
.
method = "logfoldchange"
: difference of replicate arithmetic means between developmental stages. Here, the DiffGenes functions assumes that log2a
transformed expression levels are stored in your input ExpresisonSet
.
method = "t.test"
: Welch t.test between replicate expression levels of two samples.
method = "wilcox.test"
: Wilcoxon Rank Sum Test between replicate expression levels of two samples.
method = "doubletail"
: Computes twosided pvalues by doubling the smaller tail probability (see exactTestDoubleTail
for details).
method = "smallp"
: Performs the method of small probabilities as proposed by Robinson and Smyth (2008) (see exactTestBySmallP
for details).
method = "deviance"
: Uses the deviance goodness of fit statistics to define the rejection region, and is therefore equivalent to a conditional likelihood ratio test (see exactTestByDeviance
for details).
Exclude non differentially expressed genes from the result dataset:
When specifying the alpha
argument you furthermore, need to specify the filter.method
to decide how non differentially expressed genes should be classified in multiple sample comparisons and which genes should be retained in the final dataset returned by DiffGenes
. In other words, all genes < alpha
based on the following filter.method
are removed from the result dataset.
Following extraction criteria are implemented in this function:
const
: all genes that have at least one sample comparison that undercuts or exceeds the alpha
value cut.off
will be excluded from the ExpressionSet
. Hence, for a 7 stage ExpressionSet
genes passing the alpha
threshold in 6 stages will be retained in the ExpressionSet
.
minset
: genes passing the alpha
value in ceiling(n/2)
stages will be retained in the ExpressionSet
, where n is the number of stages in the ExpressionSet
.
nset
: genes passing the alpha
value in n
stages will be retained in the ExpressionSet
. Here, the argument n
needs to be specified.
In case input ExpressionSet
objects store 0 values, internally all expression levels are
shifted by +1
to allow sufficient foldchange and pvalue computations. Additionally, a warning
is printed to the console in case expression levels have been automatically shifted.
HajkGeorg Drost
Expressed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49  data(PhyloExpressionSetExample)
# Detection of DEGs using the foldchange measure
DEGs < DiffGenes(ExpressionSet = PhyloExpressionSetExample[ ,1:8],
nrep = 2,
comparison = "below",
method = "foldchange",
stage.names = c("S1","S2","S3"))
head(DEGs)
# Detection of DEGs using the logfoldchange measure
# when choosing method = "logfoldchange" it is assumed that
# your input expression matrix stores log2 expression levels
log.DEGs < DiffGenes(ExpressionSet = tf(PhyloExpressionSetExample[1:5,1:8],log2),
nrep = 2,
comparison = "below",
method = "logfoldchange",
stage.names = c("S1","S2","S3"))
head(log.DEGs)
# Remove foldchange values < 2 from the dataset:
## first have a look at the range of foldchange values of all genes
apply(DEGs[ , 3:8],2,range)
# now remove genes undercutting the alpha = 2 threshold
# hence, remove genes having pvalues <= 0.05 in at
# least one sample comparison
DEGs.alpha < DiffGenes(ExpressionSet = PhyloExpressionSetExample[1:250 ,1:8],
nrep = 2,
method = "t.test",
alpha = 0.05,
comparison = "above",
filter.method = "nset",
n = 1,
stage.names = c("S1","S2","S3"))
# now again have a look at the range and find
# that foldchange values of 2 are the min value
apply(DEGs.alpha[ , 3:5],2,range)
# now check whether each example has at least one stage with a pvalue <= 0.05
head(DEGs.alpha)

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
All documentation is copyright its authors; we didn't write any of that.