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Mubarak hussain Syed
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30
@mubarak-hussain-syed-6451
Last seen 10.4 years ago
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