Question: DESeq2 very high p-values and padj
0
gravatar for madkitty
4.7 years ago by
madkitty580
Canada
madkitty580 wrote:

I'm comparing a control vs Treatment A and control vs.Treatment B with DESeq2 though the pvalues and padj are really high. Most padj are 0.99 or so, and most pvalues range anywhere between 0.1 to 0.9. I'm suspecting taht the way I wrote the chunk of code below doesn't compare well C vs A and C vs B,  what's wrong in the following code?..

 

# DESeq1 libraries
library( "DESeq2" )
library("Biobase")

 

r12 = read.csv("20140807_R12.csv", header = TRUE, row.names=1)

samples <- data.frame(row.names=c("C", "A", "B"), condition=as.factor(c("C", "A", "B")))

samples$condition <- relevel(samples$condition, "C")


dds <- DESeqDataSetFromMatrix(countData = as.matrix(r12), colData=samples, design=~condition)

dds$condition <- factor(dds$condition, levels =c("C", "A", "B"))

dds <- DESeq(dds)

res <- results( dds )
head (res)

DataFrame with 6 rows and 6 columns
             baseMean log2FoldChange     lfcSE       stat    pvalue      padj
            <numeric>      <numeric> <numeric>  <numeric> <numeric> <numeric>
3BHSD        1.946289    -0.13137862 0.3349360 -0.3922499 0.6948736 0.9963381
5_8S_rRNA   25.628958     0.05835918 0.4797943  0.1216338 0.9031891 0.9963381
5HT2A        2.748903    -0.08777809 0.3950686 -0.2221844 0.8241703 0.9963381
5S_rRNA   1179.943635     0.39496852 0.4627465  0.8535312 0.3933648 0.9963381
7SK       1325.918947     0.39695551 0.4538413  0.8746571 0.3817605 0.9963381
A1BG         5.639654    -0.28433104 0.4541317 -0.6260982 0.5312506 0.9963381

 

 

p-values rna-seq deseq2 • 5.9k views
ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 4.7 years ago by madkitty580
1

You are just looking at the first few genes of res. What do you get from e g

res.sig <- res[res$padj < 0.1,]

or

head(res[order(res$padj),])

?

ADD REPLYlink written 4.7 years ago by Mikael Huss4.6k

I've looked at the whole spreadsheet and there's no padj under 0.1......

ADD REPLYlink written 4.7 years ago by madkitty580

Do you really have no replicates (that's what it looks like at least)?

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by Devon Ryan89k

Indeed, we have no replicate for these samples. I don't have that issue when I run DESeq2 with replicates and multiple treatments. Is there a fix for that? ...

ADD REPLYlink written 4.7 years ago by madkitty580

If you don't have any replicate it's normal that p-values are high 

ADD REPLYlink written 4.7 years ago by Nicolas Rosewick7.5k

looks like it .. 

ADD REPLYlink written 4.7 years ago by madkitty580
5
gravatar for Devon Ryan
4.7 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

There's no fix because there's nothing to fix. I'm a little surprised you got adjusted p-values that low even. There are no meaningful p-values for your experiment because computing them would be impossible. No replicates means no meaningful p-values.

ADD COMMENTlink written 4.7 years ago by Devon Ryan89k
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