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RNA sample and array quality checking and normalization

Overview of Affymetrix GeneChip technology. An Affymetrix GeneChip microarray consists of a 1.28 cm2 glass square which is divided into a grid of about 400,000 probe cells (each about 20 24 mm x 20 24 mm). Each probe cell contains about 106 copies of one specific 25-mer oligonucleotide.There

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RNA sample and array quality checking and normalization

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    1. RNA sample and array quality checking and normalization

    2. Overview of Affymetrix GeneChip technology

    5. Data file architecture in Affymetrix Microarray Suite

    6. RNA sample quality checking

    7. (3) Assessing RNA sample quality with the Agilent Bioanalyzer:

    8. Assessing RNA quality with the Bioanalyzer

    10. Array quality checking

    12. Why we do log transformation of probe intensities

    22. Checking array quality with histograms and q-q plots

    28. Normalization/scaling

    29. Normalization/scaling Differences in the overall intensities of arrays can also be seen by plotting histograms of the probe intensities on a single plot (or the log2 of the probe intensities): The histogram of the abnormal bright array is shifted to the right Another array is also shifted to the right, but to a lesser degree

    30. Normalization/scaling

    32. Normalization/scaling

    35. Normalization to housekeeping genes

    36. Normalization to housekeeping genes

    37. Normalization to a reference RNA

    38. Normalization to a reference RNA

    39. Normalization in MAS 5.0

    40. Scaling in MAS 5.0

    41. Scaling/Normalization in MAS

    43. Non-linear scaling

    44. Non-linear scaling

    48. Normalization in dChip

    49. Conclusions

    50. Which method of normalization is best?

    51. Conclusions

    52. Conclusions

    53. Acknowledgements

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