Question: [DESeq2] Extracting results based on set thresholds
1
gravatar for nelson.s.garcia
16 months ago by
nelson.s.garcia10 wrote:

Hello,

After running DESeq and filtering using alpha = 0.05 and lfcThreshold = 1

> dds <- DESeq(dds)
> res.05_1 <- results(dds, alpha = 0.05, lfcThreshold = 1)
> summary(res.05_1)

out of 33402 with nonzero total read count
adjusted p-value < 0.05
LFC > 1.00 (up)    : 964, 2.9%
LFC < -1.00 (down) : 1228, 3.7%
outliers [1]       : 5, 0.015%
low counts [2]     : 4484, 13%
(mean count < 1)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

How do I extract the 964 upregulated and 1228 downregulated genes? Also, how do I find the information on which sample is the gene expression up or down?

Thank you very much

Nelson

deseq2 • 459 views
ADD COMMENTlink modified 16 months ago by Michael Love26k • written 16 months ago by nelson.s.garcia10
Answer: [DESeq2] Extracting results based on set thresholds
1
gravatar for Michael Love
16 months ago by
Michael Love26k
United States
Michael Love26k wrote:

The object returned by results() is a DESeqResults object, built on top of a DataFrame. It acts a lot like a simple data.frame in R.

First take a look at the column names:

res

You will also notice when you print the object like this, that it tells you at the top of the table which sample is in the numerator and which sample is in the denominator of the LFC (log2 fold change).

If you want the upregulated gene rows:

res[which(res$log2FoldChange > 0 & res$padj < .05),]

 

ADD COMMENTlink modified 16 months ago • written 16 months ago by Michael Love26k

Thanks Michael!

In my case: 

log2 fold change (MLE): Mo17M vs CMLM

Wald test p-value: Mo17M vs CMLM 

This means that the genes with l2fc positive values are upregulated in the sample Mo17M.

Is this correct?

ADD REPLYlink written 16 months ago by nelson.s.garcia10
2


Yes. If log(X/Y) > 0 then X/Y > 1 and X > Y

ADD REPLYlink written 16 months ago by Michael Love26k

Thanks Michael!

ADD REPLYlink written 16 months ago by nelson.s.garcia10
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