txt files of upregulated and down regulated genes

Question

[rthapa]

Hi, My apology if it appears to be a silly question. I wanted to save the files of upregulated and downregulated genes from DESeq2. But both of my files have lfc value of both positive and negative. I think the upregulated genes should have positive lfc value and downregulated genes should have negative lfc value.

head(resSig_AC[ order(resSig_AC$log2FoldChange, decreasing=TRUE), ] 
log2 fold change (MLE): Genotype 4611 vs 4610 
Wald test p-value: Genotype 4611 vs 4610 
DataFrame with 6 rows and 6 columns
               baseMean log2FoldChange     lfcSE      stat       pvalue         padj
              <numeric>      <numeric> <numeric> <numeric>    <numeric>    <numeric>
OS12G0234000   90.63651       22.44168  3.383756  6.041122 1.530461e-09 4.620661e-08
OS10G0366400  770.86292       12.91918  1.035700 10.542803 5.483966e-26 8.238604e-24
OS06G0491800  728.18975       12.83688  1.037314 10.447060 1.511380e-25 2.217259e-23
OS01G0512200  631.82237       12.63224  1.037406 10.248868 1.197376e-24 1.655557e-22
OS07G0258100  629.03405       12.62574  1.053737 10.083861 6.511617e-24 8.808442e-22
OS07G0582800 1421.09917       12.35930  1.030191 10.055709 8.669512e-24 1.162682e-21


tail(resSig_AC[ order(resSig_AC$log2FoldChange, decreasing=TRUE), ])
log2 fold change (MLE): Genotype 4611 vs 4610 
Wald test p-value: Genotype 4611 vs 4610 
DataFrame with 6 rows and 6 columns
              baseMean log2FoldChange     lfcSE       stat       pvalue         padj
             <numeric>      <numeric> <numeric>  <numeric>    <numeric>    <numeric>
OS03G0346150  370.9060      -12.11486  2.951741  -3.765527 1.661981e-04 1.251968e-03
OS03G0282300  437.0781      -12.35174  1.051544 -10.795307 3.622485e-27 2.789735e-25
OS01G0114100  581.6245      -12.76406  1.037175 -11.342414 8.088197e-30 7.338100e-28
OS10G0364900  639.1549      -12.90033  1.061229 -11.213719 3.492063e-29 3.075523e-27
OS03G0787600  370.6759      -26.35545  3.383485  -7.493886 6.686389e-14 1.704540e-12

Any suggestion please, where I am going wrong?

Thanks

[WouterDeCoster]

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

Could you add the code you used to save the files? I only see positive log2foldchanges in your head and only negative log2foldchanges in your tail.