Dear mailing list,



I recently found out about the new DESeq version and am currently in the process of switching my pipelines to use it. You included some sweet new features and those may simplify my life a lot. Now my questions relate to the output tables bearing the final differently expressed genes.



1.      Is there a plan to reintroduce the old DESeq 1 columns baseMeanA and baseMeanB? Or do you have some R code available to create a complete table DESeq-1-style? These two columns may be implicitly included in other values but it was just terribly useful to have them separately.

2.      If the output table is written as a tab-delimited file instead of a CSV, the first column headline is removed (since it is empty) resulting in wrong headers for all columns. See the last line of the code below. Maybe you could include some header for this column ("id" or "feature" or something similar) to prevent this behaviour?



[...]

data = read.table("counts.matrix", header=T, row.names=1, com='')

col_ordering = c(1,2,3,4)

rnaseqMatrix = data[,col_ordering]

rnaseqMatrix = round(rnaseqMatrix)

rnaseqMatrix = rnaseqMatrix[rowSums(rnaseqMatrix)>=2,]

conditions = data.frame(conditions=factor(c(rep("nha", 2), rep("nhc", 2))))

rownames(conditions) = colnames(rnaseqMatrix)

ddsFullCountTable <- DESeqDataSetFromMatrix(

    countData = rnaseqMatrix,

    colData = conditions,

    design = ~ conditions)

dds = DESeq(ddsFullCountTable)

res = results(dds)

write.table(as.data.frame(res[order(res$pvalue),]), file=deseq2_nha_nhc.txt', sep='              ', quote=FALSE, row.names=T)

[...]



[deseq2_nha_nhc.txt]

baseMean           log2FoldChange lfcSE      pvalue   padj

comp277602_c0_seq1    438.902806642428          5.58864608712407          0.302717563529963               4.20808210669443e-76  3.08662822526037e-71

[...]



Anyway thanks for the great update!



Yours hopefully,

Carsten



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