发信人: puppeteer (减肥中的河马), 信区: Biology
标 题: Re: Also microarray questions
发信站: Unknown Space - 未名空间 (Mon Nov 22 18:30:26 2004) WWW-POST

【 在 dentsu (xixi) 的大作中提到: 】
: I had done microarray and gotten the data in excel sheet. My design is
simple:
: comparison of differential gene expression in the infected cell line and
: uninfected cell line. I replicate four times for each of them. The number of
: genes shown difference is as following:
:
: 1. Based on P value:
: 10-9 ~ 10-5: 9 genes
: 10-5 ~ 10-4: 32 genes
: 10-4 ~ 10-3: 207 genes
: 10-2 ~ 0.05: 631 genes
:
: 2. Based on the fold:
: >2: 8 genes
: 1.5 ~ 2: 40 genes
: 1.0 ~ 1.5: 507 genes
:
: My questions are:
: 1.Should I use fold or P value to define the differential expression? If use
P
: value, usually what value can be used as threshold? I found someone use
10-4.
: Is P<0.05 too unstrict for microarray data?

You should use P-value. However, there is a thing called multiple hypothesis
correction. Basically, because you are testing for many genes, you can commit
an error just because of random fluctuations. As rule of thumb, divide 0.05 by
the number of genes on your chip.

: 2.How to classify those differential genes by their function? Should I use
: software to do it or just classify them one by one based on its description
in
: the excel spread sheet? If software, can I input those data directly from
the
: excel? What is the simple and most popular software to do it?

Look them up in ensemble or something. It depends on what particular
biological question in mind.

: 3.How can I write a paper for publication only based on the microarray data?

Typically you want to confirm the top few ones with PCR.

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