[BioC] Need help on understanding this error message
Fang Cheng
fc417 at nyu.edu
Fri Apr 14 20:19:10 CEST 2006
Dear all,
I was trying to load the .CEL files into R. I called affy() function.
Did not get any problem in loading it to object "dat", but when I tried
to see what's in dat, I got the following error message, which I could
not understand. Could someone give me some advices? I appreciate it in
advance!
============================================================
> dat
trying URL
'http://bioconductor.org/packages/data/annotation/1.7/src/contrib/mu11ksubacdf_1.10.0.tar.gz'
Content type 'application/x-gzip' length 621868 bytes
opened URL
==================================================
downloaded 607Kb
mkdir: cannot create directory `/usr/local/lib/R/site-library/00LOCK':
Permission denied
ERROR: failed to lock directory '/usr/local/lib/R/site-library' for
modifying
The downloaded packages are in
/tmp/RtmpuEzo5X/downloaded_packages
Error in getCdfInfo(object) : Could not obtain CDF environment, problems
encountered:
Specified environment does not contain Mu11KsubA
Library - package mu11ksubacdf not installed
Data for package affy did not contain mu11ksubacdf
Library - package mu11ksubacdf not installed
In addition: Warning messages:
1: installation of package 'mu11ksubacdf' had non-zero exit status in:
install.packages(cdfname, lib = lib, repos = Biobase:::biocReposList(),
2: cannot create HTML package index in: tools:::unix.packages.html(.Library)
AffyBatch object
size of arrays=534x534 features (22284 kb)
cdf=Mu11KsubA (??? affyids)
number of samples=10
trying URL
'http://bioconductor.org/packages/data/annotation/1.7/src/contrib/mu11ksubacdf_1.10.0.tar.gz'
Content type 'application/x-gzip' length 621868 bytes
opened URL
==================================================
downloaded 607Kb
mkdir: cannot create directory `/usr/local/lib/R/site-library/00LOCK':
Permission denied
ERROR: failed to lock directory '/usr/local/lib/R/site-library' for
modifying
The downloaded packages are in
/tmp/RtmpuEzo5X/downloaded_packages
Error in getCdfInfo(object) : Could not obtain CDF environment, problems
encountered:
Specified environment does not contain Mu11KsubA
Library - package mu11ksubacdf not installed
Data for package affy did not contain mu11ksubacdf
Library - package mu11ksubacdf not installed
In addition: Warning messages:
1: missing cdf environment ! in: show(list())
2: installation of package 'mu11ksubacdf' had non-zero exit status in:
install.packages(cdfname, lib = lib, repos = Biobase:::biocReposList(),
3: cannot create HTML package index in: tools:::unix.packages.html(.Library)
===============================================
Thank you,
Fang
----- Original Message -----
From: Gordon Smyth <smyth at wehi.edu.au>
Date: Wednesday, April 12, 2006 7:00 pm
Subject: [BioC] LIMMA: testing for batch effects
>
> >Date: Tue, 11 Apr 2006 15:08:55 +0000
> >From: Adaikalavan Ramasamy <ramasamy at cancer.org.uk>
> >Subject: [BioC] LIMMA: testing for batch effects
> >To: BioConductor mailing list <bioconductor at stat.math.ethz.ch>
> >
> >Dear all,
> >
> >We have 63 arrays that are either diseased or normal. We wish to
> select>genes adjusting for two covariates : gender (male/female) and
> >experimental batch (one/two/three).
> >
> > >From biological knowledge, we expect the batch effect to be
> significant>but we wish to quantify it numerically. Here is a way
> that we tried and
> >the problems we faced. We searched the archives without much success.
> >
> >
> > library(limma) # version 2.3.3
> > dd <- model.matrix( ~ disease + gender + batch, cl )
> > head( dd )
> > (Intercept) diseasenormal gendermale batchtwo batchthree
> > 2405 1 1 0 0 0
> > 2408 1 1 0 0 0
> > 2410 1 1 0 0 0
> > GER15 1 0 0 0 0
> > GER20 1 0 0 0 1
> > GER22 1 0 0 0 0
> >
> > fit <- lmFit(mds.rma, dd)
> >
> >
> >1) Is the following the correct way of setting up contrasts to
> find the
> >three pairwise comparison between batches ?
> >
> > contr.m <- cbind( Batch2minus1=c(0,0,0,1,0),
> Batch2minus1=c(0,0,0,0,1),>
> Batch3minus2=c(0,0,0,-1,1) )
> >
> >
> >2) From reading the LIMMA user guide, we think decideTests() could be
> >potentially useful.
> >
> > fit2 <- eBayes( contrasts.fit( fit, contr.m ) )
> > a <- decideTests( fit2, method="global" )
> > summary(a)
> > Batch2minus1 Batch2minus1 Batch3minus2
> > -1 15151 13838 4919
> > 0 26574 30561 46703
> > 1 12950 10276 3053
> >
> >Can we say that somewhere between 8000 - 27000 genes are affected
> by at
> >least one batch. Or is there a nicer/proper way of explaining this
> to a
> >biologist.
> >
> >
> >3) Ideally we would like to use method="nestedF" as suggested but
> we get
> >the following error message. Can anyone explain what might
> possibly be
> >going wrong.
> >
> > b <- decideTests( fit2, method="nestedF" )
> > Error in if (crossprod(crossprod(Q, x)) > qF[i]) { :
> > missing value where TRUE/FALSE needed
>
> This was a bug that persisted for a short time after the built-in R
> function p.adjust() changed from "fdr" to "BH" in R 2.2.0. The
> change-log entry for limma 2.3.6 reads:
>
> 6 November 2005: limma 2.3.6
>
> - decideTests() failed with method="nestedF",adjust.method="BH",
> now fixed
>
> Regards
> Gordon
>
>
> >Any hints will be much appreciated.
> >
> >Regards,
> >
> >--
> >Adaikalavan Ramasamy ramasamy at cancer.org.uk
> >Centre for Statistics in Medicine http://www.csm-oxford.org/
> >Wolfson College Annexe
> http://www.stats.ox.ac.uk/~ramasamy/>Linton Road
> Tel : 01865 284 408
> >Oxford OX2 6UD Fax : 01865 284 424
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor
mailing list