Hello , I am new to Deseq2 package and ,I am interested in differential gene expression calculations. I have two conditions Condition a (T) and Condition b (P),

Hi Syed, Low count genes are filtered automatically, see the vignette section on independent filtering. You can also filter the gene list by effect size (I.e. absolute value of log fold change). In the next release (v1.4 released on April 14) new arguments to results() allow for testing for log fold changes above a threshold which can help narrow the list of genes on effect size. Mike Hello , I am new to Deseq2 package and ,I am interested in differential gene expression calculations. I have two conditions Condition a (T) and Condition b (P), >From the Deseq-2 results after using the below mentioned commands, I get a long list of differentially expressed gene, more than 1000 unregulated and more than thousand down regulated. countsTable <- read.delim ("counts.txt", header=TRUE, row.names=1) pdata = data.frame(condition = factor(c( "T", "T", "T", "P", "P", "P", "P"))) # Three total vs four pure samples 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) Do you have any suggestions about my experiment or commands I am using to narrow down my differential gene list. Do I ned to filter low count genes or highly expressed house keeping genes, I appreciate your time. best regards Syed _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]