[BioC] Deseq2-help

[Mubarak hussain Syed]

Hi , 
I am using Deseq2 for differential gene expression calculations. I have two conditions Condition a (T) and Condition b (P), 
when I run the command using the following command lines, I get a long list of differentially expressed gene, more than 1000 unregulated and 
more than thousand down regulated. I am new to Des, do you think my command lines are good for my experiment and how could I 
narrow down my differential gene list. I appreciate your time. Thanks in advance, code is :  

> countsTable <- read.delim ("48_96_filtered.txt", header=TRUE, row.names=1)
> pdata = data.frame(condition = factor(c( "T", "T", "T", "P", "P", "P", "P")))
> library (DESeq2)
> dds <- DESeqDataSetFromMatrix(countData=countsTable, colData = pdata, design=~condition)
 colData(dds)$condition <- relevel(colData(dds)$condition, "T")

> dds <- DESeq(dds)
> results <- results(dds)
> results <- as.data.frame(results)

> sig.up.results <- results[which(results$padj < 0.05 & results$log2FoldChange > 0),]
> sig.down.results <- results[which(results$padj < 0.05 & results$log2FoldChange < 0),]

> sig.results <- results[which(results$padj < 0.05),]
> sig.results <- sig.results[order(sig.results$log2FoldChange, decreasing=TRUE),]

> plotMA(dds, pvalCutoff=0.05)

> write.table (sig.results, file= "DESeq2_Sigresultsfiltered_48_96.txt", sep= "\t ", row.names=TRUE, col.names=TRUE)
 > write.table (results, file= "DESeq2_allresults_filtered_48_96.txt", sep= "\t ", col.names=TRUE)


Best regards 
Syed 
HHMI-Institute of Neuroscience, 
1254 University of Oregon, 
Eugene, OR 97403-1254