twilight
and can be passed to functions twilight
or plot.twilight
.
twilight.pval(xin, yin, method = "fc", paired = FALSE, B = 1000, yperm = NULL, balance = FALSE, quant.ci = 0.95, s0=NULL, verbose = TRUE, filtering = FALSE)
ExpressionSet
) or a data matrix with rows corresponding to features and columns corresponding to samples. yin
can be any numerical vector of length equal to the number of samples. "fc"
for fold change equivalent test (that is log ratio test), "t"
for t-test, and "z"
for Z-test. With "pearson"
or "spearman"
, the test statistic is either Pearson's correlation coefficient or Spearman's rank correlation coefficient.method="pearson"
or method="spearman"
.yperm
have to contain the appropriate values or ranks. Use this argument carefully! If yperm
is specified, no other permutation will be done. Please note that the first row of yperm
MUST be the input vector yin
. Otherwise, the $p$-value calculation will be incorrect.method="pearson"
or method="spearman"
.quant.ci
-quantile of maximal absolute differences between each permutatin and the expected scores. method="z"
. If s0=NULL
: The fudge factor is set to the median of the pooled standard deviations.twilight.filtering
. If yperm
is specified, no filtering will be done. Note that the filtering is done on unbalanced permutations even if balance=TRUE
. twilight
object consisting of a data.frame
named result
with variables
"1"
for observations exceeding the confidence lines.observed
scores.
Scheid S and Spang R (2005): twilight; a Bioconductor package for estimating the local false discovery rate, Bioinformatics 21(12), 2921--2922.
Scheid S and Spang R (2006): Permutation filtering: A novel concept for significance analysis of large-scale genomic data, in: Apostolico A, Guerra C, Istrail S, Pevzner P, and Waterman M (Eds.): Research in Computational Molecular Biology: 10th Annual International Conference, Proceedings of RECOMB 2006, Venice, Italy, April 2-5, 2006. Lecture Notes in Computer Science vol. 3909, Springer, Heidelberg, pp. 338-347.
Storey JD and Tibshirani R (2003): Statistical significance for genomewide studies, PNAS 100(16), 9440--9445.
Tusher VG, Tibshirani R and Chu G (2001): Significance analysis of mircroarrays applied to the ionizing response, PNAS 98(9), 5116--5121.
twilight
, plot.twilight
, twilight.combi
, twilight.filtering
, expval
, twilight.teststat
### twilight object created from Golub data set
data(expval)
print(expval)
plot(expval)
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