Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
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janjoy • 0
@3e040361
Last seen 1 day ago
United States

I want to get differentially expressed genes with: [padj < 0.05 and log2FC > 1(up-regulated)] and [padj < 0.05 and log2FC < -1 (down-regulated)]. Using alpha=0.05, lfcThreshold = 1 i get far less genes compared to when I subset using res$padj < 0.05 & res$log2FoldChange > 1. I am not able to understand what's going on, even through the vignette. Would really appreciate your help!

res <- results(dds)
res

log2 fold change (MLE): condition treated vs untreated 
Wald test p-value: condition treated vs untreated 
DataFrame with 9921 rows and 6 columns
              baseMean log2FoldChange     lfcSE       stat    pvalue      padj
             <numeric>      <numeric> <numeric>  <numeric> <numeric> <numeric>
FBgn0000008   95.14429     0.00227644  0.223729   0.010175 0.9918817  0.997211
FBgn0000014    1.05652    -0.49512039  2.143186  -0.231021 0.8172987        NA
FBgn0000017 4352.55357    -0.23991894  0.126337  -1.899041 0.0575591  0.288002
FBgn0000018  418.61048    -0.10467391  0.148489  -0.704927 0.4808558  0.826834
FBgn0000024    6.40620     0.21084779  0.689588   0.305759 0.7597879  0.943501
...                ...            ...       ...        ...       ...       ...
FBgn0261570 3208.38861      0.2955329  0.127350  2.3206264  0.020307  0.144240
FBgn0261572    6.19719     -0.9588230  0.775315 -1.2366888  0.216203  0.607848
FBgn0261573 2240.97951      0.0127194  0.113300  0.1122634  0.910615  0.982657
FBgn0261574 4857.68037      0.0153924  0.192567  0.0799327  0.936291  0.988179
FBgn0261575   10.68252      0.1635705  0.930911  0.1757102  0.860522  0.967928

summary(res)

out of 9921 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up)       : 518, 5.2%
LFC < 0 (down)     : 536, 5.4%
outliers [1]       : 1, 0.01%
low counts [2]     : 1539, 16%
(mean count < 6)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results
res05 <- results(dds, alpha=0.05, lfcThreshold = 1)
summary(res05)

out of 9921 with nonzero total read count
adjusted p-value < 0.05
LFC > 1.00 (up)    : 17, 0.17% #up-regulated?
LFC < -1.00 (down) : 26, 0.26% #down-regulated?
outliers [1]       : 1, 0.01%
low counts [2]     : 0, 0%
(mean count < 1)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results
sum(res$padj < 0.05 & res$log2FoldChange > 1, na.rm=TRUE)
115 #up-regulated

sum(res$padj < 0.05 & res$log2FoldChange < -1, na.rm=TRUE)
107 #down-regulated
DifferentialExpression GeneExpression DESeq2 R • 156 views
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