Question: Proc Mixed - Differentially Expressed Genes
0
gravatar for Priyanka Surana
8.4 years ago by
Priyanka Surana0 wrote:

I am new to microarray data analysis. I am analyzing microarray experiment using PROC MIXED in SAS and use genotype, replication, time point, genotypetimepoint as fixed factors and replicationtimepoint as random factor. I want to find differentially expressed genes for each genotype*timepoint combination. Do I look at lsmeans file and associated p-values or diffs file and associated p-values.

Thanks, Priyanka

gene statistics • 2.1k views
ADD COMMENTlink modified 8.4 years ago by Priyanka Surana0 • written 8.4 years ago by Priyanka Surana0
3

You might want to consider not to use SAS... It is of course possible to do microarray statistics in SAS but the mainstream approach really is to do it in R/Bioconductor and many complete packages exist to assist you in doing so. If you are new to the field, like you say you are, I would just switch to Bioconductor and learn that, even if you have prior knowledge of SAS.

ADD REPLYlink written 8.4 years ago by Chris Evelo10.0k

Since your question is essentially about how to interpret a generalized mixed linear model and is not inherently tied to microarray data, you might consider asking it on stats.stackexchange.com, where the readership is mostly statisticians.

ADD REPLYlink written 8.4 years ago by David Quigley11k
2
gravatar for Pablo
8.4 years ago by
Pablo1.9k
Canada
Pablo1.9k wrote:

In chip analysis, R is by far the "the facto standard". I would recommend switching to R since everything is already solved there (and this is from someone that really dislikes R).

There is a brief tutorial here (chapter 6 talks about micro-arrays).

ADD COMMENTlink written 8.4 years ago by Pablo1.9k
1
gravatar for Cheng Zhongshan
8.4 years ago by
Cheng Zhongshan400 wrote:

Maybe you can try Anovarray. AnovArray is a set of SAS macros for the Analysis of Variance of Gene expression. It can be applied to the quantification of biological and technological variation and to the identification of differentially expressed genes in two or more conditions.http://www.bioinformatics.org/project/?group_id=465

ADD COMMENTlink written 8.4 years ago by Cheng Zhongshan400
0
gravatar for Priyanka Surana
8.4 years ago by
Priyanka Surana0 wrote:

Thank you everyone. They were very helpful comments and answers. I have a good starting point to go from. :) Priyanka

ADD COMMENTlink written 8.4 years ago by Priyanka Surana0
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