d******u
发帖数: 178 | 1 天呀...我都看迷糊了。
我一直用BRB ArrayTools，一个基于R的在EXCEL里面运行的免费软件。当初开始分析
microarray数据就是这么train的，所以也没仔细试过别的软件。不过想得到的分析这
个软件基本上都能做，或者能输出高水平的分析结果再用别的软件深度分析。也试过D-
CHIP，不过后来还是放弃了。GenePattern应该很牛，但还没动力整个去熟悉用法。就
跟相机一样，入了C家的门，要突然换到N家是不容易的。
扯远了。还有个比较牛的功能是，ArrayTools能直接从GEO里面下载数据并生成分析套
装，只需要输入ACCESSION NUMBER几可以了。 |
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l*****k
发帖数: 587 | 2 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 |
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d******u
发帖数: 178 | 3 常规的分析:
hierarchical clustering
PCA/MDS (Principle Component Analysis/Multi-dimensional Scaling)
class comparison (t-test/SAM)
GSEA
GO enrichment
比较好的free的网站:
NCBI Gene Expression Omnibus (GEO)
http://genechaser.stanford.edu/
软件:
D-Chip
BRB ArrayTools |
|
g***s
发帖数: 60 | 4 多谢指点，
有没有什么深入浅出的纸版的书可以推荐。
常规的分析:
hierarchical clustering
PCA/MDS (Principle Component Analysis/Multi-dimensional Scaling)
class comparison (t-test/SAM)
GSEA
GO enrichment
比较好的free的网站:
NCBI Gene Expression Omnibus (GEO)
http://genechaser.stanford.edu/
软件:
D-Chip
BRB ArrayTools |
|
l*****k
发帖数: 587 | 5 RDCOM, refer to what Arraytools has done
etc。
力？ |
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q**j
发帖数: 10612 | 6 thanks a lot. could not find arraytools, and any further suggestions or
examples? |
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l*****k
发帖数: 587 | 7 google nci arraytools
they have a pretty comprehensive software package using excel as interface,
with
R and fortran at backend
it is free for academic users. |
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l*****k
发帖数: 587 | 8 arraytools has a plug in, not sure if it is in R though |
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a****o
发帖数: 1786 | 9 【 以下文字转载自 Biology 讨论区 】
发信人: dadiayou (Shorthair), 信区: Biology
标 题: Re: 请教microarray的数据分析
发信站: BBS 未名空间站 (Tue Mar 2 15:56:18 2010, 美东)
常规的分析:
hierarchical clustering
PCA/MDS (Principle Component Analysis/Multi-dimensional Scaling)
class comparison (t-test/SAM)
GSEA
GO enrichment
比较好的free的网站:
NCBI Gene Expression Omnibus (GEO)
http://genechaser.stanford.edu/
软件:
D-Chip
BRB ArrayTools |
|
