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When predictions were performed on the same dataset, comparison between predictive abilities from different models was performed with Hotelling-Williams test [ 64], using the R script developed by Christensen et al. [ 65].
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Furthermore, dataset comparisons between the transcriptomes of primary tumor cells and prostate cancer cell lines, which were established from metastatic lesions and showed unique CD expression [ 10, 11], demonstrated that they were not representative of cells in primary tumors.
Two sources of data were used to gauge the effort involved in the manual curation process, and although differences exist between the types of activities involved in generating the two datasets, comparison between rates of curation in each allows us to determine the effort for the completion of various curation tasks.
Dataset comparison was carried out between SP, 5D3 (04-126) and EC, ES.
Since the same cell line (MCF-7) and same treatment period (6 h) were used to generate the above dataset as the CMAP dataset, comparison analysis can be done between the two datasets.
Furthermore, for both the cell line dataset and a publicly available third dataset, a comparison between ANOVA-based array and treatment effect sizes revealed that the treatment effects are much larger.
These datasets allowed comparison between gene expression in peripheral blood mononuclear cells (PBMCs), neutrophils or synovial fluid monocytes (SFM) (Additional file 2: Table S2).
The Venn diagram (Fig. 2) shows overlapping differentially expressed genes between different dataset comparisons.
In doing so we determined that all 73 probe sets covering 54 changes in gene expression displayed conserved directionality between the two dataset comparisons (p < 10-5).
Samples were scaled by setting the average intensity of the middle 96%% of all probe-set signals to a fixed value of 100 for every sample in the dataset, allowing comparisons between micro-arrays.
θ, ωPAML and genetic divergence were also estimated in the North American VAX004 gp120 dataset [50] for comparison between B subtypes (Table 1).
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