Leuk_18

Quantile normalized gene expression data (Affymetrix HG-U133 Plus 2.0 array) from the MILE (Microarray Innovations In LEukemia) program [1] (ArrayExpress, accession number E-GEOD-13159)

Data pre-processing and all analyses were conducted using the open-source statistical software R v3.4.3 (R Core Team, 2017a). Raw microarray data from stage I of the MILE study included 2,096 .CEL files that contained 16 acute and chronic leukemia subclasses, myelodysplastic syndromes (MDSs), and “none of the target classes” control group that included non-leukemia and healthy bone marrow. Data preparation included two main steps, namely cleaning and transformation. To perform a quality assessment for Affymetrix GeneChip data, we using the R package affy. The homogeneous distribution of signal and intensities and assessment of RNA degradation were checked. The samples were removed with dataset if their value of mean signal intensities was different than: $\pm3 \sigma$ and if threshold value for the 3. /5 ratios more then 3 for $\beta$-actin, and 1.25 for GAPDH (criterium recommended by Affymetrix). Next, we calculated the normalized values with robust rma background correction, quantile normalization, and median polish. To achieve a normal or near-normal distribution, the log2 transformation of gene expression data was performed .  After this transformation of the data, the dataset consisted of 2,077 samples and 54675 probes.

1. Kohlmann A, Kipps TJ, Rassenti LZ, Downing JR, Shurtleff SA, Mills KI, Gilkes AF, Hofmann WK, Basso G, Dell'orto MC, Foà R, Chiaretti S, De Vos J, Rauhut S, Papenhausen PR, Hernández JM, Lumbreras E, Yeoh AE, Koay ES, Li R, Liu WM, Williams PM, Wieczorek L, Haferlach T. An international standardization programme towards the application of gene expression profiling in routine leukaemia diagnostics: the Microarray Innovations in LEukemia study prephase. Br J Haematol. 2008 Sep;142(5):802-7. doi: 10.1111/j.1365-2141.2008.07261.x. PMID: 18573112; PMCID: PMC2654477.