Dear community,

I am using DESeq2 to perform my differential expression analyses. My
question is, I think, very simple. To interprete the results if I have:

> 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?

Thanks for your time.
Best,
Alicia


--
Alicia R. Pérez-Porro
PhD candidate

Giribet lab
Department of Organismic and Evolutionary Biology
MCZ labs
Harvard University
26 Oxford St, Cambridge MA 02138
phone: +1 617-496-5308
fax: +1 617-495-5667
www.oeb.harvard.edu/faculty/giribet/

Department of Marine Ecology
Center for Advanced Studies of Blanes (CEAB-CSIC)
C/Accés Cala St. Francesc 14
17300 Blanes, Girona, SPAIN
phone: +34 972 336 101
fax: +34 972 337 806
www.ceab.csic.es

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