发信人: leohawk (leohawk), 信区: Biology
标 题: Re: Also microarray questions
发信站: Unknown Space - 未名空间 (Tue Nov 23 14:04:35 2004), 转信

1. what algorithm did you use to calculate the P value? Each method may
give a different P value magnitude.

2. Affymetrix netaffyx has a GO tool, it is kinda useful.

3. It is very hard to publish in good journals with ONLY microarray
data now. You need to do more work to confirm your array data. I
personally don't belive in PCR confirmation.

4. I would suggest you do a permutation based analysis, one tool you can
use is ArrayTools from NCI Biometrix group.

Good Luck

【 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?
: 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?
: 3.How can I write a paper for publication only based on the microarray data?
: I am new for microarray although I know how it works. Since there is no expert
: to get instruction in my department, I make little progress after I had spend
: lots of time on those data. Hope here I can get good advises. Thank you.


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