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(Ambion Applied Biosystems, Darmsta
(Ambion Applied Biosystems, Darmstadt, Germany). cRNA quality was assessed by capillary electrophoresis on Agilent 2 100 Bioanalyzer (Agilent Technologies). Expression levels of > 48 000 mRNA transcripts were assessed by Human-WG6v2 Expression BeadChip (Illumina, Eindhoven, The Netherlands). Hybridization was carried out according to the manufacturer's instructions. Genomewide SNP data had been generated from genomic DNA using the HumanHap300 Genotyping BeadChip (Illumina) with 318 237 SNPs as described before. (24) A comparison with the microarray platforms used in the Seattle study is shown in Figure 1. All data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE32504 (http://www.ncbi.nlm. nih.gov/geo/query/acc.cgi?acc=GSE32504).
Preprocessing and quality control
Illumina BeadStudio version 3.0 (Illumina, San Diego, CA, USA) was used for all low-level preprocessing steps of the expression data, including background estimation and correction, normalization and probe set summary. After these low-level preprocessing steps, 9875 genes with high detection P-value (>0.1) or >10% missing values were filtered out and removed from the data set. (25) The remaining missing signal intensities were estimated using the 'k nearest neighbor' algorithm implemented in R BioConductor. (26,27) The resulting data set was subsequently log2 transformed. Finally, after all preprocessing steps, the raw data of 48 701 probe signal intensities were mapped and reduced to signal intensities corresponding to 15 439 unique genes.
Preprocessing and quality control
Illumina BeadStudio version 3.0 (Illumina, San Diego, CA, USA) was used for all low-level preprocessing steps of the expression data, including background estimation and correction, normalization and probe set summary. After these low-level preprocessing steps, 9875 genes with high detection P-value (>0.1) or >10% missing values were filtered out and removed from the data set. (25) The remaining missing signal intensities were estimated using the 'k nearest neighbor' algorithm implemented in R BioConductor. (26,27) The resulting data set was subsequently log2 transformed. Finally, after all preprocessing steps, the raw data of 48 701 probe signal intensities were mapped and reduced to signal intensities corresponding to 15 439 unique genes.
0/5000
(Ambion diterapkan Biosystems, Darmstadt, Jerman). kualitas cRNA dinilai oleh Elektroforesis kapiler di Bioanalyzer Agilent 2 100 (Agilent Technologies). Tingkat ekspresi mengatakan 48 000 mRNA transkrip dinilai oleh manusia-WG6v2 ekspresi BeadChip (Illumina, Eindhoven, Belanda). Hibridisasi dilaksanakan sesuai dengan instruksi dari pabriknya. Genomewide SNP data yang telah dihasilkan dari DNA genom menggunakan HumanHap300 genotipe BeadChip (Illumina) dengan 318 237 SNP seperti yang dijelaskan sebelumnya. (24) perbandingan dengan platform microarray yang digunakan dalam penelitian Seattle ditunjukkan dalam gambar 1. Semua data telah disimpan di Omnibus ekspresi gen NCBI's dan dapat diakses melalui nomor induk GEO seri GSE32504 (http://www.ncbi.nlm. nih.gov/Geo/query/ACC.cgi?ACC=GSE32504).
preprocessing dan kontrol kualitas
Illumina BeadStudio versi 3.0 (Illumina, San Diego, CA, USA) digunakan untuk semua tingkat rendah preprocessing langkah ekspresi data, termasuk latar belakang estimasi dan koreksi, normalisasi dan probe set ringkasan. Setelah ini rendah preprocessing langkah, 9875 gen dengan tinggi deteksi P-nilai (mengatakan 0.1) atau mengatakan 10% nilai-nilai yang hilang disaring dan dihapus dari kumpulan data. (25) sisa hilang sinyal intensitas diperkirakan menggunakan algoritma 'k terdekat tetangga' dilaksanakan di R BioConductor. (26,27) kumpulan data yang dihasilkan pada log2 berubah. Akhirnya, setelah semua langkah preprocessing, data mentah dari 48 701 probe sinyal intensitas yang dipetakan dan mengurangi intensitas sinyal sesuai dengan 15 439 unik gen.
preprocessing dan kontrol kualitas
Illumina BeadStudio versi 3.0 (Illumina, San Diego, CA, USA) digunakan untuk semua tingkat rendah preprocessing langkah ekspresi data, termasuk latar belakang estimasi dan koreksi, normalisasi dan probe set ringkasan. Setelah ini rendah preprocessing langkah, 9875 gen dengan tinggi deteksi P-nilai (mengatakan 0.1) atau mengatakan 10% nilai-nilai yang hilang disaring dan dihapus dari kumpulan data. (25) sisa hilang sinyal intensitas diperkirakan menggunakan algoritma 'k terdekat tetangga' dilaksanakan di R BioConductor. (26,27) kumpulan data yang dihasilkan pada log2 berubah. Akhirnya, setelah semua langkah preprocessing, data mentah dari 48 701 probe sinyal intensitas yang dipetakan dan mengurangi intensitas sinyal sesuai dengan 15 439 unik gen.
Sedang diterjemahkan, harap tunggu..
(Ambion Applied Biosystems, Darmstadt, Germany). cRNA quality was assessed by capillary electrophoresis on Agilent 2 100 Bioanalyzer (Agilent Technologies). Expression levels of > 48 000 mRNA transcripts were assessed by Human-WG6v2 Expression BeadChip (Illumina, Eindhoven, The Netherlands). Hybridization was carried out according to the manufacturer's instructions. Genomewide SNP data had been generated from genomic DNA using the HumanHap300 Genotyping BeadChip (Illumina) with 318 237 SNPs as described before. (24) A comparison with the microarray platforms used in the Seattle study is shown in Figure 1. All data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE32504 (http://www.ncbi.nlm. nih.gov/geo/query/acc.cgi?acc=GSE32504).
Preprocessing and quality control
Illumina BeadStudio version 3.0 (Illumina, San Diego, CA, USA) was used for all low-level preprocessing steps of the expression data, including background estimation and correction, normalization and probe set summary. After these low-level preprocessing steps, 9875 genes with high detection P-value (>0.1) or >10% missing values were filtered out and removed from the data set. (25) The remaining missing signal intensities were estimated using the 'k nearest neighbor' algorithm implemented in R BioConductor. (26,27) The resulting data set was subsequently log2 transformed. Finally, after all preprocessing steps, the raw data of 48 701 probe signal intensities were mapped and reduced to signal intensities corresponding to 15 439 unique genes.
Preprocessing and quality control
Illumina BeadStudio version 3.0 (Illumina, San Diego, CA, USA) was used for all low-level preprocessing steps of the expression data, including background estimation and correction, normalization and probe set summary. After these low-level preprocessing steps, 9875 genes with high detection P-value (>0.1) or >10% missing values were filtered out and removed from the data set. (25) The remaining missing signal intensities were estimated using the 'k nearest neighbor' algorithm implemented in R BioConductor. (26,27) The resulting data set was subsequently log2 transformed. Finally, after all preprocessing steps, the raw data of 48 701 probe signal intensities were mapped and reduced to signal intensities corresponding to 15 439 unique genes.
Sedang diterjemahkan, harap tunggu..
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