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Old 03-04-2014, 12:52 AM   #1
unique379
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Location: Italy

Join Date: Aug 2012
Posts: 27
Post Performing ANOVA test for NGS time sereis datasets

Dear all,

May be its very basic question for you all.
I would like to perform 2 way ANOVA test for my NGS time series counts data. It is raw data counts by HT-Seq. I have 2 condition and for each corresponding diff. time points and their counts. Suggestion is to perform 2 way anova test. but problem is, i don't know the better way to prepare file for that in order to use R function like aov(). Help me to do so....

My raw counts (without normalization) like..

gene_name counts_value (for each condition and corresponding time points (36 sample in total) )

gene_1 2349
gene_2 3462380
gene_3 0
gene_4 123

Query:
1) How to prepare (format of input) input file in order to use R functions
2) is there any package (bioconductor or R) to perform this analysis
3) may i have to normalize this raw counts before performing 2 way ANOVA
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Old 03-04-2014, 01:09 AM   #2
dpryan
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Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,478
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Cross-posted on biostars, where I already replied.
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bioconductor, bioinfomatics, microarray, ngs

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