Question: Annotate Package: How do I get the gene names and how do I write my matrix
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gravatar for James W. MacDonald
15.0 years ago by
United States
James W. MacDonald50k wrote:
If you are planning on using R for any more analysis, you would do well to read some of the documentation that comes with R and the BioC packages rather than hoping that a good samaritan will help you do things. 1.) Look at the documentation for the annaffy package 2.) Read 'An Introduction to R' 3.) Read 'An Introduction to R' All of this information is easily accessible by typing help.start() at an R prompt. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> S Peri <biocperi@yahoo.com> 08/18/04 01:54PM >>> Dear group, I did SAM, T-test analyses and obtained p-values. Now, these files look like these: T-test Values: > Gli_X0_X1_pvals[1:5] 100_g_at 1000_at 1001_at 1002_f_at 1003_s_at 0.80033009 0.31943016 0.33078591 0.05216239 0.08957325 Fold change(Avg. Diff): > MyBrain_X0_X1_Exp_FCs[1:5] 100_g_at 1000_at 1001_at 1002_f_at 1003_s_at 1.0176023 0.9274588 0.8752550 1.1056984 1.1096023 My question: Using annotation package how can I convert the probe ID's to Gene names. how do i incorporate gene name in place of 100_g_at? 2. How can I choose/filter P-values from T-test that are less than 0.01 to 0 ? 3. How can write the values into a table with 3 colnames: Gene, P-value, Fold change I am doing this for first time. Please help me. Thank you. Regards, PS _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
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