adj.P metod = "BH" many exact the same value

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Guest User ★ 13k

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Dear list, I was converting the p values of my DEG list to adjusted p-values (using benjamin Hochberg) and found out that many adjusted p-values have the exact same value. (using topTable from limma package) Is this normal and what is the reason for this observation? thanks in advance, cheers, Bas -- output of sessionInfo(): R version 2.15.3 (2013-03-01) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.14.4 affy_1.36.1 Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affyio_1.26.0 BiocInstaller_1.8.3 preprocessCore_1.20.0 tools_2.15.3 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.

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ADD COMMENT • link updated 11.7 years ago by Michael Love 43k • written 11.7 years ago by Guest User ★ 13k

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Steve Lianoglou ★ 13k

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Hi, On Thursday, April 4, 2013, Bas ter Braak [guest] wrote: > > Dear list, > > I was converting the p values of my DEG list to adjusted p-values (using > benjamin Hochberg) and found out that many adjusted p-values have the exact > same value. (using topTable from limma package) > Is this normal and what is the reason for this observation? Are the identical values that you observe equal to 1 by any chance? -- Steve Lianoglou Defender of The Thesis | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted]]

ADD COMMENT • link 11.7 years ago Steve Lianoglou ★ 13k

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Hi Steve, Thanks for your reply. No, the adjusted p-values are not equal to 1. Although the regular p-values vary from 0.0000225 to 0.000769, the adjusted p-values are exactly 0.069652712348149. And this for 147 DEGs. Is there something wrong with my code in R? thanks, Bas On Thu, Apr 4, 2013 at 4:13 PM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Hi, > > > On Thursday, April 4, 2013, Bas ter Braak [guest] wrote: > >> >> Dear list, >> >> I was converting the p values of my DEG list to adjusted p-values (using >> benjamin Hochberg) and found out that many adjusted p-values have the exact >> same value. (using topTable from limma package) >> Is this normal and what is the reason for this observation? > > > Are the identical values that you observe equal to 1 by any chance? > > > > -- > Steve Lianoglou > Defender of The Thesis > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > [[alternative HTML version deleted]]

ADD REPLY • link 11.7 years ago Bas ter Braak ▴ 20

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hi Bas,

This is a direct consequence of the method of Benjamini and Hochberg. The paper is quite accessible and worth a look:

http://www.jstor.org/stable/2346101

See formula (1) under "False Discovery Rate Controlling Procedure".

All the p-values p_i up to p_k also get rejected at the FDR q. for a visualization of this formula, take a few sorted p-values with adjusted p-value written above:

p <- sort(c(.01,.2,.21,.22,.5,.51,.52,.8,.9))
padj <- p.adjust(p, method="BH")
plot(p,ylim=c(0,1),xlim=c(0,length(p)))
text(seq_along(p),p,round(padj,3),pos=3)
abline(0,padj[4]/length(p))

here, k = 4, m=length(p), and q = padj[4].

Mike

ADD REPLY • link 11.7 years ago • updated 9.6 years ago Michael Love 43k

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thanks Mike, this was very helpful! On Fri, Apr 5, 2013 at 12:58 PM, Michael Love <michaelisaiahlove@gmail.com>wrote: > hi Bas, > > This is a direct consequence of the method of Benjamini and Hochberg. The > paper is quite accessible and worth a look: > http://www.jstor.org/stable/2346101 > > See formula (1) under "False Discovery Rate Controlling Procedure". > > All the p-values p_i up to p_k also get rejected at the FDR q. > > for a visualization of this formula, take a few sorted p-values with > adjusted p-value written above: > > p <- sort(c(.01,.2,.21,.22,.5,.51,.52,.8,.9)) > padj <- p.adjust(p, method="BH") > plot(p,ylim=c(0,1),xlim=c(0,length(p))) > text(seq_along(p),p,round(padj,3),pos=3) > abline(0,padj[4]/length(p)) > > here, k = 4, m=length(p), and q = padj[4]. > > > Mike > > > > On Fri, Apr 5, 2013 at 10:16 AM, Bas ter Braak <basterbraak@gmail.com>wrote: > >> Hi Steve, >> >> Thanks for your reply. No, the adjusted p-values are not equal to 1. >> Although the regular p-values vary from 0.0000225 to 0.000769, the >> adjusted >> p-values are exactly 0.069652712348149. And this for 147 DEGs. Is there >> something wrong with my code in R? >> thanks, >> >> Bas >> On Thu, Apr 4, 2013 at 4:13 PM, Steve Lianoglou < >> mailinglist.honeypot@gmail.com> wrote: >> >> > Hi, >> > >> > >> > On Thursday, April 4, 2013, Bas ter Braak [guest] wrote: >> > >> >> >> >> Dear list, >> >> >> >> I was converting the p values of my DEG list to adjusted p-values >> (using >> >> benjamin Hochberg) and found out that many adjusted p-values have the >> exact >> >> same value. (using topTable from limma package) >> >> Is this normal and what is the reason for this observation? >> > >> > >> > Are the identical values that you observe equal to 1 by any chance? >> > >> > >> > >> > -- >> > Steve Lianoglou >> > Defender of The Thesis >> > | Memorial Sloan-Kettering Cancer Center >> > | Weill Medical College of Cornell University >> > Contact Info: http://cbio.mskcc.org/~lianos/contact >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]

ADD REPLY • link 11.6 years ago Bas ter Braak ▴ 20

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