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This article mainly explains "how to use affy package to view full matching probe and mismatch probe". The explanation in this article is simple and clear and easy to learn and understand. please follow the editor's train of thought to study and learn "how to use affy package to view full matching probe and mismatch probe".

In addition to full matching (perfect match, pm) probes (25-mer probes) for fluorescence signal detection, affymetrix expression microarray sometimes designs mismatched (mismatch, mm) probes (one site mismatch). The design based on PM-MM probe can greatly improve the specificity and sensitivity of detecting low concentration target sequences, and facilitate background correction. Due to the different methods of processing the original data of the chip, sometimes the mismatched probe signal is used, and sometimes the mismatched probe information is not referenced. For example, the common RMA algorithm for data standardization does not make use of the mm signal value, while the mas5 method should refer to mm for calculation.

Therefore, in the process of actual analysis, it is necessary to make clear whether the corresponding affymetrix chip contains two kinds of probe signals, and whether the standardized analysis methods of the original data can be matched with each other.

In the process of analysis, we can read the original data of the affymetrix chip, and the corresponding AffyBatch object uses the pm () function and mm () to check whether it contains the corresponding two kinds of probe signal values.

GSM1616746_Pool_1_Hilscher_26-07-2012.CEL.gz GSM1616747_Pool_1_Reif-Hilscher_8-2-2012.CEL.gz369707 390205 GSM1616748_Pool_1wdh_Reif-Hilscher_9-2-2012.CEL.gz GSM1616749_Pool_2_Hilscher_26-07-2012.CEL.gz369707 181,497 GSM1616750_Pool_2_Reif-Hilscher_8-2-2012.CEL.gz GSM1616751_Pool_2wdh_Reif-Hilscher_9-2-2012.CEL.gz369707 223 190 GSM1616752_Pool_3_Hilscher_26-07-2012.CEL.gz GSM1616753_Pool_3_Reif-Hilscher_8-2-2012.CEL.gz369707 525240 GSM1616754_Pool_3wdh_Reif-Hilscher_9-2-2012.CEL.gz GSM1616755_Pool _ 4_Hilscher_26-07-2012.CEL.gz369707 192446 GSM1616756_Pool_4_Reif-Hilscher_8-2-2012.CEL.gz GSM1616757_Pool_4wdh_Reif-Hilscher_9-2-2012.CEL.gz369707 214155 GSM1616746_Pool_1_Hilscher_26-07-2012.CEL.gz GSM1616747_Pool_1_Reif-Hilscher_8-2-2012.CEL.gz370871 174157 GSM1616748_Pool_1wdh_Reif -Hilscher_9-2-2012.CEL.gz GSM1616749_Pool_2_Hilscher_26-07-2012.CEL.gz370871 159215 GSM1616750_Pool_2_Reif-Hilscher_8-2-2012.CEL.gz GSM1616751_Pool_2wdh_Reif-Hilscher_9-2-2012.CEL.gz370871 148137 GSM1616752_Pool_3_Hilscher_26-07-2012.CEL.gz GSM1616753_Pool_3_Reif-Hilscher_8-2-2012.CEL.gz370871 213 180 GSM1616754_Pool_3wdh_Reif-Hilscher_9-2-2012.CEL.gz GSM1616755_Pool_4_Hilscher_26-07-2012.CEL.gz370871 15234 GSM1616756_Pool_4_Reif-Hilscher_8-2-2012.CEL.gz GSM1616757_Pool_4wdh_Reif-Hilscher 9-2-2012.CEL.gz370871 151134Thank you for your reading The above is the content of "how to use the affy package to view the full matching probe and mismatch probe". After the study of this article, I believe you have a deeper understanding of the problem of how to use the affy package to view the full matching probe and mismatch probe. Here is, the editor will push for you more related knowledge points of the article, welcome to follow!

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