[R] lapack routines cannot be loaded [Help request]
Dear BioConductor and R fellow users I apologize in advance for double posting, but I am not sure which list would actually be best fit for this message. I am experiencing a weird error with my R installation on Ubuntu 10.04.4 (LTS) 64bit: When I run R on the terminal everything goes smoothly: $R R version 2.15.2 (2012-10-26) -- "Trick or Treat" Copyright (C) 2012 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. However, as soon as I try to use limma (or WGCNA... I haven't tried other packages yet) the following mistake pops up ( lapack routines cannot be loaded ) >library(limma) > fit <- lmFit(Data.rma, design) Error in chol2inv(fit$qr$qr, size = fit$qr$rank) : lapack routines cannot be loaded In addition: Warning message: In chol2inv(fit$qr$qr, size = fit$qr$rank) : unable to load shared object '/usr/lib64/R/modules//lapack.so': /usr/lib64/R/modules//lapack.so: undefined symbol: dpstrf_ > It is independent of the dataset I am using. I have already tried to recompile the whole BioConductor set of packages, and updated the general packages via CRAN, but nothing changed. Following I am attaching my sessionInfo(), and you will find enclosed to this email the (incriminated) lapack.so file, should you be willing/able to take a look at it. Any insights into what could be going on, and how to address the issue? > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8LC_MESSAGES=en_US.utf8 [7] LC_PAPER=CLC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_3.12.3 hgu133plus2cdf_2.10.0 AnnotationDbi_1.18.4 [4] affy_1.34.0 Biobase_2.16.0BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 BiocInstaller_1.4.9 DBI_0.2-5 [4] IRanges_1.14.4preprocessCore_1.18.0 RSQLite_0.11.2 [7] stats4_2.15.2 tools_2.15.2 zlibbioc_1.2.0 Thank you in advance, Marco -- Dr Marco Manca University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: UNS40 West building - 5th floor Room5.544, Universiteit Singel 40, 6229 HX Maastricht E-mail: m.ma...@maastrichtuniversity.nl Office telephone: +31(0)433884289 Personal mobile: +31(0)626441205 Twitter: @markomanka * This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or doctor-patient/consultant-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA *__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R: [BioC] samr - extract genes from siggenes.table
I am not sure about this... I think they have logFC larger than 2... you are
simply seeing them in scientific notation.
Why don't you try setting the option scipen (penalty for scientific notation)
"on the high side"?
Something like:
> options(scipen = 50)
should be more than enough...
Anyway, most likely other people can give you better hints.
All the best, Marco
--
Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)
Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
Visiting address: Experimental Vascular Pathology group, Dept of Pathology -
Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX
Maastricht
E-mail: m.ma...@maastrichtuniversity.nl
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka
*
This email and any files transmitted with it are confidential and solely for
the use of the intended recipient.
It may contain material protected by privacy or attorney-client privilege. If
you are not the intended recipient or the person responsible for
delivering to the intended recipient, be advised that you have received this
email in error and that any use is STRICTLY PROHIBITED.
If you have received this email in error please notify us by telephone on
+31626441205 Dr Marco MANCA
*
Da: bioconductor-boun...@r-project.org [bioconductor-boun...@r-project.org] per
conto di Assa Yeroslaviz [fry...@gmail.com]
Inviato: mercoledì 9 febbraio 2011 17.35
A: bioconductor; R help forum
Oggetto: [BioC] samr - extract genes from siggenes.table
Hi BioC user,
I have a problem extracting the gene set I would like to work with.
Here is I work with my data:
normData <- read.delim("normalizedData.txt",sep ="\t")
# two class unpaired comparison
# y must take values 1,2
classes <- c(-1,-2,1,2)
#prepere the data for the samr analysis
data.x <-as.matrix(normData[,8:11])
d=list(x=data.x,y=classes,
geneid=as.character(normData[,1]),genenames=as.character(normData[,1]),
logged2=TRUE)
samr.obj<-samr(d, resp.type="Two class paired", nperms=100)
delta.table <- samr.compute.delta.table(samr.obj)
delta=0.4
siggenes.table<-samr.compute.siggenes.table(samr.obj,delta, d,
delta.table,min.foldchange=2)
genes.up <- as.data.frame(siggenes.table$genes.up)
genes.down <- as.data.frame(siggenes.table$genes.lo)
the data set I am working with has four column of two experiments. when
running the samr.compute.siggenes.table command I get
> str(siggenes.table)
List of 5
$ genes.up : chr [1:9769, 1:8] "6587" "865" "22929" "10172" ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:8] "Row" "Gene ID" "Gene Name" "Score(d)" ...
$ genes.lo : chr [1:10788, 1:8] "10836" "22277" "1243" "10509"
...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:8] "Row" "Gene ID" "Gene Name" "Score(d)" ...
$ color.ind.for.multi: NULL
$ ngenes.up : int 9769
$ ngenes.lo : int 10788
So I guess I have 9769 up-regulated and 10788 down-regulated genes. The
problem is, that not all of them are above 2fold:
> head(siggenes.table$genes.up)
Row Gene ID Gene Name Score(d)
[1,] "6587" "NM_001142426_at" "NM_001142426_at" "670.084615384572"
[2,] "865" "NM_000946_at""NM_000946_at""581.731543624152"
[3,] "22929" "NM_147134_at""NM_147134_at""469.481132075439"
[4,] "10172" "NM_003640_at""NM_003640_at""296.630872483217"
[5,] "10956" "NM_004484_at""NM_004484_at""284.233163028334"
[6,] "28444" "XM_001125699_at" "XM_001125699_at" "281.629310344832"
Numerator(r) Denominator(s+s0) Fold Change
[1,] "435.555""0.6500041" "*1.30352619041372e+131*"
[2,] "433.39" "0.7450012" "2.90663046260321e+130"
[3,] "248.825""0.5300037" "8.01288059495468e+74"
[4,] "220.99" "0.7450012" "3.34671508906627e+66"
[5,] "3059.77""10.76499" "Inf"
[6,] "163.345""0.571" "*1.48506219251034e+49*"
q-value(%)
[1,] "0"
[2,] "0"
[3,] "0"
[4,] "1.95405681104834"
[5,] "1.95405681104834"
[6,] "1.95405681104834"
@What do I need the parameter min.foldchage if it is not a filter to
extract genes with a fold induction value lower than 2?
I would like to know how do I extract a subset of matrix from inside a list?
my siggenes.table is a list with two matrices inside. I would like to filter
these matrices for genes with a 2fold up- and down-regulation.
Thanks
Assa
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
[R] R: "biplot" graphical options?
Thanks Andris, Michael and Petr for your prompt and kind feedbacks.
I will try generating my own biplot from low-level graph commands... I hope it
will work.
Best regards,
Marco
--
Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)
PO Box 616
6200 MD Maastricht
E-mail: m.ma...@path.unimaas.nl
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka
*
This email and any files transmitted with it are confidential and solely for
the use of the intended recipient.
It may contain material protected by privacy or attorney-client privilege. If
you are not the intended recipient or the person responsible for
delivering to the intended recipient, be advised that you have received this
email in error and that any use is STRICTLY PROHIBITED.
If you have received this email in error please notify us by telephone on
+31626441205 Dr Marco MANCA
*
Da: andris.jankev...@gmail.com [andris.jankev...@gmail.com] per conto di Andris
Jankevics [an...@osi.lv]
Inviato: mercoledì 2 settembre 2009 14.31
A: Manca Marco (PATH)
Cc: r-help@r-project.org
Oggetto: Re: [R] "biplot" graphical options?
Hi, You can make a biplot on Your own, it is not so hard. And in this
case You can change parameters for every low level function as You
wish.
PC <- prcomp (iris[,1:4])
lambda <- PC$sdev * sqrt(nrow(PC$x))
plot (t(t(PC$x)/lambda),pch=16,col=as.numeric(iris[,5]))
par (new=T)
Rot <- t(t(PC$rotation)*lambda)
XLIM <- c(-max(abs(Rot[,1])),max(abs(Rot[,1])))
XLIM <- XLIM+(XLIM*0.1)
plot(Rot,col=4,axes=FALSE,xlim=XLIM,ylim=XLIM,pch="")
arrows (rep(0,nrow(PC$rotation)),rep(0,nrow(PC$rotation)),Rot[,1],Rot[,2],col=4)
text (Rot[,1:2],rownames(Rot),col=6)
axis (3)
axis (4)
Best regards,
Andris
On Wed, Sep 2, 2009 at 1:02 PM, Manca Marco
(PATH) wrote:
>
> Dear R-help fellows
>
> good afternoon.
>
> I am struggling in the attempt to impose some graphical conditions (changing
> point symbols, colors, etc) to biplot function (I am using it to visualize
> the results of princomp) but I can't apparently manage to change anything but
> the axis... and I have been browsing manuals and vignettes without finding
> any explicit suggestions on how to operate...
>
> Can anyone, please, point my attention to the relevant documentation?
>
> Thank you in advance and best regards,
> Marco
>
> --
> Marco Manca, MD
> University of Maastricht
> Faculty of Health, Medicine and Life Sciences (FHML)
> Cardiovascular Research Institute (CARIM)
> PO Box 616
> 6200 MD Maastricht
>
> E-mail: m.ma...@path.unimaas.nl
> Office telephone: +31(0)433874633
> Personal mobile: +31(0)626441205
> Twitter: @markomanka
>
>
> *
>
> This email and any files transmitted with it are confide...{{dropped:15}}
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] "biplot" graphical options?
Dear R-help fellows
good afternoon.
I am struggling in the attempt to impose some graphical conditions (changing
point symbols, colors, etc) to biplot function (I am using it to visualize the
results of princomp) but I can't apparently manage to change anything but the
axis... and I have been browsing manuals and vignettes without finding any
explicit suggestions on how to operate...
Can anyone, please, point my attention to the relevant documentation?
Thank you in advance and best regards,
Marco
--
Marco Manca, MD
University of Maastricht
Faculty of Health, Medicine and Life Sciences (FHML)
Cardiovascular Research Institute (CARIM)
PO Box 616
6200 MD Maastricht
E-mail: m.ma...@path.unimaas.nl
Office telephone: +31(0)433874633
Personal mobile: +31(0)626441205
Twitter: @markomanka
*
This email and any files transmitted with it are confide...{{dropped:15}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
