Displaying 20 results from an estimated 1000 matches similar to: "limma, FDR, and p.adjust"
2004 Dec 20
1
[BioC] limma, FDR, and p.adjust
You asked the same question on the Bioconductor mailing list back in August. At that time, you
suggested yourself a solution for how the adjusted p-values should be interpreted. I answered
your query and told you that your interpretation was correct. So I'm not sure what more can be
said, except that you should read the article Wright (1992), which is cited in the help entry for
p.adjust(),
2004 Dec 20
1
Re: [BioC] limma, FDR, and p.adjust
Mark,
there is a fdr website link via Yoav Benjamini's homepage which is: http://www.math.tau.ac.il/%7Eroee/index.htm
On it you can download an S-Plus function (under the downloads link) which calculates the false discovery rate threshold alpha level using stepup, stepdown, dependence methods etc.
Some changes are required to the plotting code when porting it to R. I removed the
2005 Jan 16
1
p.adjust(<NA>s), was "Re: [BioC] limma and p-values"
I append below a suggested update for p.adjust().
1. A new method "yh" for control of FDR is included which is valid for any
dependency structure. Reference is Benjamini, Y., and Yekutieli, D. (2001).
The control of the false discovery rate in multiple testing under
dependency. Annals of Statistics 29, 1165-1188.
2. I've re-named the "fdr" method to "bh" but
2005 Jul 14
2
Partek has Dunn-Sidak Multiple Test Correction. Is this the same/similar to any of R's p.adjust.methods?
The Partek package (www.partek.com) allows only two selections for Multiple
Test Correction: Bonferroni and Dunn-Sidak. Can anyone suggest why Partek
implemented Dunn-Sidak and not the other methods that R has? Is there any
particular advantage to the Dunn-Sidak method?
R knows about these methods (in R 2.1.1):
> p.adjust.methods
[1] "holm" "hochberg" "hommel"
2005 Nov 28
4
Games-Howell, Gabriel, Hochberg
Hello,
I read a book about statistics in psychology. The authors use SPSS. They
talk about post hoc tests after ANOVA finds significant effects:
- Gabriel's procedure (for equal or slightly different sample sizes)
- Hochberg's GT2 (for different sample sizes)
- Games-Howell procedure (for populations with unequal variances)
I could not find them in R. Do they not exist in R
2010 Aug 08
1
p.adjust( , fdr)
Hello,
I am not sure about the p.adjust( , fdr). How do these adjusted p-values
get?
I have read papers of BH method. For independent case, we compare the
ordered p-values with the alfa*i/m, where m is the number of tests. But I
have checked that result based on the adjusted p-values is different with
that by using the independent case method.
Then how do the result of p.adjust( , fdr) come?
And
2009 Mar 18
0
p.adjust(p, n) for n>length(p)
Hi all,
I am having a problem with the function "p.adjust" in stats. I have looked at the manuals and searched the R site, but didn't get anything that seems directly relevant. Can anybody throw any light on it or confirm my suspicion that this might be a bug?
I am trying to use the p.adjust() function to do Benjamini/Hochberg FDR control on a vector of p-values that are the
2008 Jan 15
0
FDR for hypergeometric tests
Dear list,
I have performed several tests for the hypergeometric distribution
using phyper() for some gene annotation categories as follows
>phyper(26,830,31042,337, lower.tail=F)
>phyper(16,387,31042,337, lower.tail=F)
.
.
.
I am only running some selected categories but I would like to correct
this value for multiple testing since I
have 3121 possible tests according to 3121
2010 Feb 07
1
p.adjust.Rd sugggestion
L.S.
In the current version of ?p.adjust.Rd, one needs
to scroll down to the examples section to find
confirmation of one's guess that "fdr" is an
alias of "BH".
Please find a patch in attachment which mentions
this explicitly.
Best,
Tobias
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2007 Feb 28
2
topTable function from LIMMA
Dear R-Help,
I am using the function "topTable" from the LIMMA package. To estimate
adjusted P-values there are several options (adjust="fdr" , adjust="BH")
as shown below:
topTable(fit, number = 10, adjust = "BH", fit$Name)
I guess any of these options (fdr, BH, etc.) is using a default of
FDR=0.05 which is quite conservative (i.e., very
2004 Dec 21
0
Fwd: problems with limma
On Wed, December 22, 2004 12:11 am, r.ghezzo at staff.mcgill.ca said:
> ----- Forwarded message from r.ghezzo at staff.mcgill.ca -----
> Date: Mon, 20 Dec 2004 15:45:11 -0500
> From: r.ghezzo at staff.mcgill.ca
> Reply-To: r.ghezzo at staff.mcgill.ca
> Subject: [R] problems with limma
> To: r-help at stat.math.ethz.ch
>
> I try to send this message To Gordon
2004 Dec 20
2
problems with limma
I try to send this message To Gordon Smyth at smyth at vehi,edu.au but it bounced
back, so here it is to r-help
I am trying to use limma, just downloaded it from CRAN. I use R 2.0.1 on Win XP
see the following:
> library(RODBC)
> chan1 <- odbcConnectExcel("D:/Data/mgc/Chips/Chips4.xls")
> dd <- sqlFetch(chan1,"Raw") # all data 12000
> #
> nzw <-
2005 Jan 08
1
p.adjust(<NA>s), was "Re: [BioC] limma and p-values"
>>>>> "GS" == Gordon K Smyth <smyth@wehi.edu.au>
>>>>> on Sat, 8 Jan 2005 01:11:30 +1100 (EST) writes:
<.............>
GS> p.adjust() unfortunately gives incorrect results when
GS> 'p' includes NAs. The results from topTable are
GS> correct. topTable() takes care to remove NAs before
GS> passing
2011 Oct 04
1
a question about sort and BH
Hi,
I have two questions want to ask.
1. If I have a matrix like this, and I want to figure out the rows whose
value in the 3rd column are less than 0.05. How can I do it with R.
hsa-let-7a--MBTD1 0.528239197 2.41E-05
hsa-let-7a--APOBEC1 0.507869409 5.51E-05
hsa-let-7a--PAPOLA 0.470451884 0.000221774
hsa-let-7a--NF2 0.469280186 0.000231065
hsa-let-7a--SLC17A5
2003 Nov 03
1
FDR in p.adjust
Hello,
I've a question about the fdr method in p.adjust: What is the threshold of
the FDR, and is it possible to change this threshold?
As I understand the FDR (please correct) it adjusts the p-values so that for
less than N% (say the cutoff is 25%) of the alternative hypothesis the Null
is in fact true.
thanks a lot for help,
+regards,
Arne
2014 Nov 27
0
p.adjust on a vector including NA values
dear all,
I recently came across the following issue and I was not sure whether it is intentionally or not:
using p.adjust to adjust p-values for multiple hypothesis testing using the method from Benjamini and Hochberg removes all NA values from the input vector and does not account for them in the adjustment, i.e. in a vector of 23 p-values with 20 of them being NA it adjusts the 3 non-NA
2010 Jul 13
6
permutation-based FDR
Hola a todos,
Tengo un pequeño problemilla...
Tengo unas 9000 variables que he contrastado con 1 en concreto con el test
de wilcoxon. He calculado el p-valor, y queria corregirlo con el
permutation-based FDR. He encontrado una funcion con R comp.fdr()que hace
esta corrección, pero te pide que le pongas las variables con las
observaciones y te hace el test (según he entendido). Yo solo quiero
2011 Sep 30
1
Hi
Hi,
There is a question that I am confused.
I have a set of data like this:
hsa-miR-205--GATA3 0.797882767 1.08E-13
hsa-miR-205--ITGB4 0.750217593 1.85E-11
hsa-miR-187--PGF 0.797604155 3.24E-11
hsa-miR-205--SERPINB5 0.744124886 3.28E-11
hsa-miR-205--PBX1 0.734487224 7.89E-11
hsa-miR-205--MCC 0.72499934 1.80E-10
hsa-miR-205--WNT5B 0.717705259 3.33E-10
hsa-miR-200c--PKN2 0.721746815
2012 May 04
0
LIMMA decideTests result zero from contrast matrix
Dear All,
I am using the LIMMA package to create 2 contrasts for my data and then calculating the vennCounts of the decideTests from the contrast.fit to be able to create venn Diagrams.
The code works fine but the summary(results) shows zeros for all i.e. no gene were up regulated or downregulated. This is not true for my data since toptable output shows Log fold change greater than > 2.
I am
2006 Jun 28
0
Help with topTable function in limma
Hello,
I have just completed an analysis of microarray data using the limma package. The analysis appears to have worked fine. However, when I use the topTable function to get the significant genes, I get the following error:
> topTable(fit2,coef=5,adjust="fdr")
Error in array(x, c(length(x), 1), if (!is.null(names(x))) list(names(x), :
attempt to set an attribute on NULL