用了旧的CNV芯片还用旧的参考基因组

文章发表在 Breast Cancer Res. 2017; 19: 30.

Published online 2017 Mar 16. doi: 10.1186/s13058-017-0825-6

样本量并不少： case-control study of breast cancer diagnosed before age 40 years (200 cases, 293 controls) Continue reading →

看起来只是一个摘要，并没有相关文章出来： http://ascopubs.org/doi/abs/10.1200/jco.2015.33.15_suppl.579 Continue reading →

多批次WES数据该肿么办

批次很多时候无法避免，比如文章 Biomed Res Int. 2014 . doi: 10.1155/2014/319534 就提到：

In large WES studies, some samples are occasionally sequenced twice or even more times due to a variety of reasons, for example, insufficient coverage in the first experiment, sample duplication, and the rest. It is challenging how to best utilize these duplicated exomes for SNP discovery and genotype calling, especially with batch effects taken into consideration.

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网上的答案经常不靠谱

通常情况下我会使用 featureCounts 得到表达矩阵是 raw counts, 但总是有人需要我转换成各种形式，比如 RPKM, FPKM and TPM Continue reading →