By José Osorio y Fortéa et al., 2007 (submitted for publication). Download AffyGCQC distribution. See AffyGCQC Documentation. See AffyGCQC Supplementary Information.
Please enter the project name
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Please enter the array type
AG (Arabidopsis) ATH1-121501 (Arabidopsis) DrosGenome1 (Drosophila) HG-U133A (Human) HG-U133B (Human) HG-U133_Plus_2 (Human) HG-U95Av2 (Human) HG-U95B (Human) HG-U95C (Human) HG-U95D (Human) HG-U95E (Human) MG-U74Av2 (Mouse) Mouse430A (Mouse) Mouse430B (Mouse) Mouse430_2 (Mouse) RAE230A (Rat) RAE230B (Rat) RG-U34A (Rat) RG-U34B (Rat) RG-U34C (Rat)
Please enter the tissue type
Adrenal Brain Breast Cerebellum Colon Cotyledon Dendritic Cells Flower Heart Hypocotyl Intestine Kidney Leaf Liver Lung Lymph Node Macrophages Muscle Ovary Prostate Rectum Root Rosette Seed Shoot Apex Silique Spleen Skin Stomach Testes Thymus Thyroid Other
Please select the compressed (.zip) file containing your RPT files
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AffyGCQC Informations:
Enter the project and the user names. This information will appear in the first page of the AffyGCQC output file. Please, avoid blanks and special characters
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Enter the array type. If the array type is not listed, please send an e-mail to affygcqc@biologie.ens.fr and it will be implemented in the program.
Enter the tissue type. If the tissue type is not listed, please send an e-mail to affygcqc@biologie.ens.fr and it will be added in the list. This information does not appear in the output, it is just used to get an idea of the studied tissue types.
Select the compressed (.zip) file containing your RPT files. RPT files (see example) are report files produced by GCOS software (minimum number of files to perform extreme studentized deviate tests for outlier detection is 3 for G1 and G2 tests and 4 for G3 test). If you have more than 20 files, please send an email to affygcqc@biologie.ens.fr and it will be implemented in the program. Please avoid blanks for the directory and the file names.
Enter your e-mail. The program output will be sent to this e-mail address. Your e-mail is not stored. Therefore, if you wish to register for AffyGCQC mailing list, please send an e-mail to affygcqc@biologie.ens.fr
AffyGCQC has been submitted for publication. AffyGCQC: GeneChip Data Quality Control (José Osorio y Fortéa et~al., 2007).
Affymetrix GeneChip® oligonucleotide arrays are dedicated to analyzing gene expression differences across distinct experimental conditions. Data production for such arrays is an elaborate process with many potential sources of variability unrelated to biologically relevant gene expression variations. Therefore, rigorous data quality assessment is fundamental throughout the process for downstream biologically meaningful analyses. We have thus developed a program named AffyGCQC which is the acronym for a bioinformatics tool designed to perform Affymetrix GeneChip Quality Control (QC). This program implements a graphical representation of the QC metrics recommended by Affymetrix for GeneChip oligonucleotide array technology. Most importantly, it performs extreme studentized deviate statistical tests for the set of arrays being compared in a given experiment, thus providing an objective measure for outlier detection. AffyGCQC has been designed as an easy-to-use web-based interface (online supplementary information: www.transcriptome.ens.fr/AffyGCQC).