[BioC] DESeq2: up- and down-regulated genes

[Simon Anders]

Hi Alicia

On 26/05/14 01:39, Alicia R. Pérez-Porro wrote:
>> mcols(res, use.names=TRUE) ##To know the level of conditions
> DataFrame with 6 rows and 2 columns
>                         type                                description
>                  <character>                                <character>
> baseMean       intermediate                the base mean over all rows
> log2FoldChange      results log2 fold change (MAP): condition SP vs EB
> lfcSE               results         standard error: condition SP vs EB
> stat                results         Wald statistic: condition SP vs EB
> pvalue              results      Wald test p-value: condition SP vs EB
> padj                results                       BH adjusted p-values
>
> By exporting my up-regulated genes doing:
>
> write.table(as.data.frame(resSig[ order( -resSig$log2FoldChange,
> -resSig$baseMean ),]),
>            file="UpRegulated.txt")
>
> Are my genes up-regulated in the EB condition? or in the SP condition?

Have a look at the column description: It says "log2 fold change (MAP): 
condition SP vs EB".

With "SP vs EB", we mean that SP was compared against EB. Hence: 
positive sign means stronger in SP than in EB.

 > What about this example: (generated with
 > write.table(as.data.frame(resSig[
 > order( -resSig$log2FoldChange, -resSig$baseMean ),]),
 >          file="UpRegulated.txt")

Please show us how you generated 'resSig' from 'res', and how tyou got 
'res' from your DESeqDataset object.

BTW, if you can your e-mail program to not wrap the lines, this would 
make it much more readable.

   Simon