请教一个NGS read count LOESS normalization的问题 - 未名空间MITBBS历史存档

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请教一个NGS read count LOESS normalization的问题

请教一个NGS read count LOESS normalization的问题# Biology - 生物学

v*e2015-10-07 07:10

1 楼

【以下文字转载自 Joke 讨论区】
发信人: repeating (randomly), 信区: Joke
标题: 替同学的清华EMBA班征一个Bay Area的女性旅友 (转载)
发信站: BBS 未名空间站 (Tue Jul 20 00:50:46 2010, 美东)
发信人: ghost2004 (游泳的大灰狼), 信区: SanFrancisco
标题: 替同学的清华EMBA班征一个Bay Area的女性旅友
发信站: BBS 未名空间站 (Tue Jul 20 00:01:27 2010, 美东)
大学好友的EMBA班过来学习，顺便在这里旅游。计划的行程是SF - Lake Tahoe -
Yosemite - Monterey - Half Moon Bay - SF，自驾游。
他们一行15个人，只有一个女孩子。鉴于这些人英语沟通能力都有限，在这里的朋友也
没时间陪他们，所以在这里帮他们征一个女性旅友。一切食宿他们负责，保证住宿有一
定档次的酒店，全部结束后，再给 300$。
（有人觉得价格低，也可以适当商量。不过我们毕竟找的不是专业导游，如果哪位暑期正好没事

z*t2015-10-07 07:10

2 楼

【以下文字转载自 Chicago 讨论区】
发信人: zlltt (人生苦短抓紧性感), 信区: Chicago
标题: 超级萌无敌萌----《彩虹糖的梦》
发信站: BBS 未名空间站 (Sat Jul 30 14:20:27 2011, 美东)
不萌你给我包子

A*H2015-10-07 07:10

3 楼

我要normalize NGS read count with GC-content
这里有一篇文章
http://journals.plos.org/plosone/article?id=10.1371/journal.pon
中间有些不懂。看了些网站教材，还不是很懂，到这里问一下。只有包子答谢了。
GC-content correction
第一句
To correct for sequencing biases that arise due to preferential sequencing
of certain levels of GC content, we normalize the read depth based on the GC
content of each bin.
第二句
These values incorporate mapability information, such that we only consider
the GC content of mappable bases.
第三句
To correct the data, we first calculate the average read depth for bins with
GC content in intervals of 0.1%.
第四句
We then use the LOESS method to fit a regression line to this data.
第五句
The correction value for each bin is equal to the difference between the
median read depth and the average read depth of that bin.
第六句
We then scale the values such that the correction is neutral with respect to
the total number of reads.
请问一下，这第五句和第六句哪里用到了LOESS的结果？第五句是说，对于每一个bin，
把median-average作为correction value，然后第六句怎么scale the values呢？是不
是这里scale要用到LOESS的predict？
谢谢

z*n2015-10-07 07:10

4 楼

娘男们，世界是你们的了，老娘是out了。。

a*r2015-10-07 07:10

5 楼

第五句

A*H2015-10-07 07:10

6 楼

能展开说说吗？谢谢

【在 a**r 的大作中提到】

: 第五句

a*r2015-10-07 07:10

7 楼

You are welcome on Oct.21
http://kresgeeye.org/research/ligon-research-center-of-vision/
Kresge Eye Institute, in association with the Anatomy/Cell Biology
Department, is organizing its second annual Vision Research Workshop on Oct.
21. This workshop highlights research accomplishments of our graduate
students, postdoctoral fellows, residents and clinical fellows. The goal is
to provide an outstanding opportunity for the vision community on the WSU
campus to interact with each other and exchange ideas for possible
collaboration.
Kang Zhang, M.D., Ph.D., professor of Ophthalmology, chief of Ophthalmic
Genetics, University of California San Diego, has agreed to be our clinical
translational research lecturer for this workshop.
At this time,,,,,,

A*H2015-10-07 07:10

8 楼

您这云里雾里的我不知所云啊。。。

Oct.
is

【在 a**r 的大作中提到】

: You are welcome on Oct.21
: http://kresgeeye.org/research/ligon-research-center-of-vision/
: Kresge Eye Institute, in association with the Anatomy/Cell Biology
: Department, is organizing its second annual Vision Research Workshop on Oct.
: 21. This workshop highlights research accomplishments of our graduate
: students, postdoctoral fellows, residents and clinical fellows. The goal is
: to provide an outstanding opportunity for the vision community on the WSU
: campus to interact with each other and exchange ideas for possible
: collaboration.
: Kang Zhang, M.D., Ph.D., professor of Ophthalmology, chief of Ophthalmic