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[mRNA-seq] 求问高手,DESeq2筛选转录组数据,用去除表达量为0的数据吗

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发表于 2018-8-12 10:05:14 | 显示全部楼层 |阅读模式
我用DESeq2筛选转录组数据,用去除表达量为0的数据吗?另外,DESeq2是不是不用标准归一化,但是我看到做heatmap时,却要归一化,为什么?



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发表于 2018-8-13 21:09:42 | 显示全部楼层
目测是不看说明文档就操作,这两个问题的答案在DEseq2包的使用说明中都有啊DEseq2.html.仔细看一看就可以找到了.
比如:
Pre-filtering

While it is not necessary to pre-filter low count genes before running the DESeq2 functions, there are two reasons which make pre-filtering useful: by removing rows in which there are very few reads, we reduce the memory size of the dds data object, and we increase the speed of the transformation and testing functions within DESeq2. Here we perform a minimal pre-filtering to keep only rows that have at least 10 reads total. Note that more strict filtering to increase power is automatically applied via independent filtering on the mean of normalized counts within the results function.

Input data
Why un-normalized counts?


As input, the DESeq2 package expects count data as obtained, e.g., from RNA-seq or another high-throughput sequencing experiment, in the form of a matrix of integer values. The value in the i-th row and the j-th column of the matrix tells how many reads can be assigned to gene i in sample j. Analogously, for other types of assays, the rows of the matrix might correspond e.g. to binding regions (with ChIP-Seq) or peptide sequences (with quantitative mass spectrometry). We will list method for obtaining count matrices in sections below.

The values in the matrix should be un-normalized counts or estimated counts of sequencing reads (for single-end RNA-seq) or fragments (for paired-end RNA-seq). The RNA-seq workflow describes multiple techniques for preparing such count matrices. It is important to provide count matrices as input for DESeq2’s statistical model (Love, Huber, and Anders 2014) to hold, as only the count values allow assessing the measurement precision correctly. The DESeq2 model internally corrects for library size, so transformed or normalized values such as counts scaled by library size should not be used as input.
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发表于 2018-8-16 23:36:05 | 显示全部楼层
金恩12 发表于 2018-8-13 21:09
目测是不看说明文档就操作,这两个问题的答案在DEseq2包的使用说明中都有啊DEseq2.html.仔细看一看就可以找 ...

能主动看文档的,已经太少太少了,唉
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