Accounting for one-channel depletion improves missing value imputation in 2-dye microarray data.

Background: For 2-dye microarray platforms, some missing values may arise from an un-measurably low RNA expression in one channel only. Information of such "one-channel depletion" is so far not included in algorithms for imputation of missing values.

Results: Calculating the mean deviation between imputed values and duplicate controls in five datasets, we show that KNN-based imputation gives a systematic bias of the imputed expression values of one-channel depleted spots.

Gene expression profilers and conventional clinical markers to predict distant recurrences for premenopausal breast cancer patients after adjuvant chemotherapy.

A large proportion of breast cancer patients are treated with adjuvant chemotherapy after the primary operation, but some will recur in spite of this treatment. In order to achieve an improved and more individualised therapy, our knowledge in mechanisms for drug resistance needs to be increased. We have investigated to what extent cDNA microarray measurements could distinguish the likelihood of recurrences after adjuvant CMF (cyclophosphamide, methotrexate and 5-fluorouracil) treatment of premenopausal, lymph node positive breast cancer patients, and have also compared this with the corresponding performance when using conventional clinical variables.

Molecular signatures in childhood acute leukemia and their correlations to expression patterns in normal hematopoietic subpopulations.

Global expression profiles of a consecutive series of 121 childhood acute leukemias (87 B lineage acute lymphoblastic leukemias, 11 T cell acute lymphoblastic leukemias, and 23 acute myeloid leukemias), six normal bone marrows, and 10 normal hematopoietic subpopulations of different lineages and maturations were ascertained by using 27K cDNA microarrays. Unsupervised analyses revealed segregation according to lineages and primary genetic changes, i.e.

"Good Old" clinical markers have similar power in breast cancer prognosis as microarray gene expression profilers.

We compared the power of gene expression measurements with that of conventional prognostic markers, i.e., clinical, histopathological, and cell biological parameters, for predicting distant metastases in breast cancer patients using both established prognostic indices (e.