Background adjustment using sequence information
Gcrma adjusts for background intensities in Affymetrix array data which include optical noise and non-specific binding (NSB). The main function gcrma converts background adjusted probe intensities to expression measures using the same normalization and summarization methods as a Robust Multiarray Average (RMA). Gcrma uses probe sequence information to estimate probe affinity to NSB. The sequence information is summarized in a more complex way than the simple GC content. Instead, the base types (A, T, G or C) at each position along the probe determine the affinity of each probe. The parameters of the position-specific base contributions to the probe affinity is estimated in an NSB experiment in which only NSB but no gene-specific binding is expected.
| System | Target | Derivation | Build status |
|---|---|---|---|
| x86_64-linux | /gnu/store/jqjjiyin42d1sjd8mz4vbacwxfw589q4-r-gcrma-2.68.0.drv | ||
| riscv64-linux | /gnu/store/knd1c1zjjzn5b83wg9qhvkn3frgvh7wz-r-gcrma-2.68.0.drv | ||
| powerpc-linux | /gnu/store/559q4h25msdbrd2xn2jzs9cjav69chzv-r-gcrma-2.68.0.drv | ||
| powerpc64le-linux | /gnu/store/vir4h9fmi5fd9z0bhc61fs4xclv7x4yp-r-gcrma-2.68.0.drv | ||
| mips64el-linux | /gnu/store/ip6zdqphs8pmjxd8pqa0yqp919m8kzmf-r-gcrma-2.68.0.drv | ||
| i686-linux | /gnu/store/ra6ghk8fvx80kfpk11nixic5q0znd9pi-r-gcrma-2.68.0.drv | ||
| i586-gnu | /gnu/store/ycwzdzyifha31jgysiz0aaknklphmnda-r-gcrma-2.68.0.drv | ||
| armhf-linux | /gnu/store/mmgg06l4cj7ys34hdhbzyhyp105zadc3-r-gcrma-2.68.0.drv | ||
| aarch64-linux | /gnu/store/gzrlz7ndqpa00s31rvsjv5k5gh70blbz-r-gcrma-2.68.0.drv |
| Linter | Message | Location |
|---|---|---|
| No lint warnings ✓ | ||