Computational protocol: QPRT: a potential marker for follicular thyroid carcinoma including minimal invasive variant; a gene expression, RNA and immunohistochemical study

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Protocol publication

[…] Statistical analysis was performed with the statistical computing environment R []. Additional software packages (ab1700, rma, multtest) were taken from the Bioconductor project [].Probe level normalization was conducted using the quantile normalization method [].Probeset summarization was calculated using the robust median polish method [] on the normalized data. For each probeset an additive robust additive model on the logarithmic scale (base 2) was fitted across the arrays, considering the different affinities of the probes via the probe effect. We used a global filter to reduce the dimension of the microarray data: We applied an intensity filter (the signal intensity of a probe set should be above 100 in at least 25 percent of the samples, if the group size is equal) and a variance filter (the interquartile range of log2 intensities should be at least 0.5).p-values were calculated applying the two sample t-test (assuming equal variances in both groups) to identify genes that are differentially expressed between the two groups. We use the False Discovery Rate (FDR) [] to account for multiple testing. Also Fold Changes (FC) between the two groups were calculated for each gene. Differentially expressed genes were determined with p-value, FDR and FC criteria.Unsupervised hierarchical cluster analysis was performed with the agglomeration method „average“. Manhattan method is used for the distance measure. Probe sets with a standard deviation more than one were included in the clustering. The results of immunohistochemical staining were analyzed with a Pearson's Chi-Square test, using SPSS 8.0 (SPSS Inc., Chicago, USA).Sensitivity is defined as positive stained carcinomas in relation to all carcinomas included in the study. Specificity is the fraction of carcinomas in all positively immunostained samples. […]

Pipeline specifications

Software tools multtest, SPSS
Applications Miscellaneous, Gene expression microarray analysis
Diseases Adenoma, Carcinoma, Neoplasms, Thyroid Neoplasms