Bioconductor Forum

Hello, I'm using a small data of 10 people to work with GENESIS and generate relatedness using PC-relate function. I generate .gds file, create kinship using KING. When generating principal components I get error  `` Error in acc(object, NL[cnode]) : unmatched node provided   `` R 3.4.2 \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#--Code begins <code>bed<-"…

genesis pcair

updated 7.6 years ago • GENOMIC_region

duplicated levels in factors are deprecated 3: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, ... : duplicated levels in factors are deprecated 4: In `levels<-`(`*tmp*`, value = if (nl == nL...duplicated levels in factors are deprecated 5: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, ... :…

R riboseqr ribosome profiling

updated 10.2 years ago • ohtack9

x = "log2_fold_change", y = "adj_p", title = "Edu+ vs EdU- Microglia", xlim = c(-8,10), ylim = c(0,8), selectLab = c(), pCutoff = 0.05, FCcutoff = 0.5849, labSize = 5.…

EnhancedVolcano

updated 4.0 years ago • acharest

site/bcbostoned/ for more information. Questions: email stvjc at channing dot harvard dot edu </div

updated 16.2 years ago • Vincent J. Carey, Jr.

and git. Experience with Bioconductor a plus. Contact stvjc at channing dot harvard dot edu for more details

genetics genomics software Job

updated 5.2 years ago • Vincent J. Carey, Jr.

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 </div

updated 17.2 years ago • Anjan Purkayastha

59012201, 59020799] | 902 Warning messages: 1: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste(labels, : duplicated levels will not be allowed in factors anymore 2: In `levels<-`(`*tmp*`, value...if (nl == nL) as.character(labels) else paste(labels, : duplicated levels will not be allowed in factors anymore > dim(allorigins) [1...…

GenomicRanges GenomicRanges

updated 12.7 years ago • Guest User

not contain NAs In addition: Warning messages: 1: In \`levels<-\`(\`\*tmp\*\`, value = if (nl == nL) as.character(labels) else paste0(labels,  :   duplicated levels in factors are deprecated 2: In \`levels<-\`(\`\*tmp\*\`, value...if (nl == nL) as.character(labels) else paste0(labels,  :   duplicated levels in factors are deprecated…

riboseqr ribosome profiling

updated 9.8 years ago • alper.celik

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 </div

vsn vsn

updated 17.2 years ago • Anjan Purkayastha

with probes attributed to the Hthgu133ahsrefseq - CDF files (http://brainarray.mbni.med.umich .edu/Brainarray/Database/CustomCDF/13.0.0/refseq.asp). On the other hand I'm using CNV-data from agilent (Agilent Human Genome

cdf cdf

updated 15.2 years ago • Noemi Andor

vector with unique names In addition: Warning message: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels, : duplicated levels in factors are deprecated</pre>   This is a related thread

software error easyrnaseq genomicalignments bam

updated 10.3 years ago • Michael Dondrup

in the preinstalled data but when i try my own i get the error Error in split.default(names(sort(nl)), f.index): first argument must be a vector I have found some similar post/problems but i still cannot identify the issue. Im...0 GO terms and 0 relations. ) Nothing to do: Error in split.default(names(sort(nl)), f.index): first argument must be a vector Traceback: 1. new("top…

topGO GO

updated 3.0 years ago • peter

Type][1] I'm interested in comparing: ```r 1. LI-P-L vs LI-NP 2. LI-P-L vs HV 3. LI-P-L vs LI-P-NL 4. LI-P-NL vs HV ``` Based on the plot, do you think it makes sense to split these into 4 separate matrices, or simply use the contrast

DESeq2

updated 4.5 years ago • Tash.

<div class="preformatted">(sending again now that I'm a member of the list) There appears to be a broken link in the "Sources Of Data" section of the Bioconductor web page. The "Unigene Annotation For Affy Chips" link doesn't work. The most obvious error is the lack of ".edu" at the end of the domain name. However, inserting that doesn't restore the link either. Also, how is it decided wh…

Annotation affy Annotation affy

updated 23.5 years ago • Colin A. Smith

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 </div

TimeCourse timecourse TimeCourse timecourse

updated 16.7 years ago • Anjan Purkayastha

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 </div

Normalization Normalization

updated 16.3 years ago • Anjan Purkayastha

59020799] | 902 > Warning messages: > 1: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste(labels, : > duplicated levels will not be allowed in factors anymore > 2: In `levels<-`(`*tmp...value = if (nl == nL) as.character(labels) else paste(labels, : > duplicated levels will not be allowed in factors any…

rtracklayer GenomicRanges rtracklayer GenomicRanges

updated 12.6 years ago • Valerie Obenchain

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 </div

probe tilingArray probe tilingArray

updated 17.2 years ago • Anjan Purkayastha

or any other command when a background R job is run? R --min-vsize=vl --max-vsize=vu --min-nsize=nl --max-nsize=nu --max- ppsize=N source: http://stat.ethz.ch/R-manual/R-patched/library/base/html/Memory.html Thx Carol [[alternative

updated 16.7 years ago • carol white

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 =========================================== </div

tilingArray tilingArray

updated 17.2 years ago • Anjan Purkayastha

of your best papers and name/contact information of three references to Dr. Wei Li (WL1 at bcm dot edu) with email subject "Postdoctoral application". [[alternative HTML version deleted]] </div

updated 17.1 years ago • Wei Li

due date for applications is _August 21st. _Please send applications to gustin.s AT wehi DOT edu DOT au and put SCHOLARSHIP in the subject line. We hope to see you there

sequencing transcription epigenomics visualization infrastructure News

updated 10.4 years ago • Matthew Ritchie

student Erasmus MC Department of Pathology JNI,Room H Be-302 Dr. Molewaterplein 50 3015 GE Rotterdam-NL phone: +3110-7043093 fax: +3110-7044762 r.kandimalla at erasmusmc.nl http://www.erasmusmc.nl/pathologie </div

GO convert GO convert

updated 17.2 years ago • r.kandimalla

van Amsterdam Faculty of Science IBED/AMB (Aquatische Microbiologie) Nieuwe Achtergracht 127 NL-1018WS Amsterdam the Netherlands tel. + 31 20 5257060 fax + 31 20 5257064 </div

biomaRt biomaRt

updated 19.6 years ago • krasikov@science.uva.nl

cledit iconv TRUE TRUE TRUE TRUE TRUE TRUE NLS profmem cairo ICU long.double libcurl TRUE FALSE TRUE TRUE TRUE TRUE ~ Bogdan

TCL/TK

updated 4.2 years ago • Bogdan

for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 </div

Transcription Normalization probe tilingArray Transcription Normalization probe tilingArray

updated 17.1 years ago • Anjan Purkayastha

<div class="preformatted">Bioconductor basics course in Boston, 24-25 October -- space is limited Tentative agenda --- Oct 24 (Monday) 9am-12pm Vince Carey (VJC, bioconductor core): introduction, software setup, basic programming and structures, annotation 12pm-1pm (lunch on your own) 1pm-4pm Aedin Culhane (Dana Farber Cancer Institute): on clustering/ordination, reproducibility 4pm…

Genetics Cancer Genetics Cancer

updated 14.3 years ago • Vincent J. Carey, Jr.

img alt="Bienvenue chez Meilleur Mobile" border="0" src="http://www.meilleurmobile.com/images/nl/bienvenue/header.gif"/></a></h1> <div style="margin: 5px 0 0 0 ;"><img alt="économisez BEAUCOUP d'argent" border="0" src="http://www.meilleurmobile.com...images/nl/bienvenue/titre1.gif"/></div> <div style="margin: 0px 0px 0 0px; padding: 5px 8px 0 12px; font-size: 1…

updated 17.2 years ago • Laure de Meilleurmobile

van Amsterdam Faculty of Science IBED/AMB (Aquatische Microbiologie) Nieuwe Achtergracht 127 NL-1018WS Amsterdam the Netherlands tel. + 31 20 5257089 fax + 31 20 5257064 </div

Normalization limma Normalization limma

updated 20.2 years ago • Nataliya Yeremenko

interests, pdfs of papers, and contact information for three references to peter_park[at]harvard[dot]edu. -- ---------------------------------------------------------------------- Peter J. Park Children's Hospital/Harvard Medical School 77 Avenue Louis Pasteur 255D, Boston, MA 02115 617-525-4468 http

Microarray Microarray

updated 18.9 years ago • Peter J Park

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com

updated 14.3 years ago • Guido Hooiveld

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

Annotation biomaRt Annotation biomaRt

updated 17.5 years ago • Guido Hooiveld

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

updated 16.9 years ago • Guido Hooiveld

function(x) unlist(strsplit(x," "))[1]) group_list <- factor(group_list,levels = c("NL","PCOS")) table(group_list) # change ID names gpl <- getGEO('GPL570', destdir=".") probe.gene <- Table(gpl)[,c("ID","Gene Symbol")] colnames(probe.gene...exp.unique) fit <- lmFit(exp.unique, design) contrast.matrix <- makeContrasts(paste0(c("NL","PCOS"), collaps…

GEOquery ArrayExpress limma DifferentialExpression

updated 20 months ago • SSSJec

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

miRNA cdf miRNA cdf

updated 16.5 years ago • Guido Hooiveld

van Amsterdam Faculty of Science IBED/AMB (Aquatische Microbiologie) Nieuwe Achtergracht 127 NL-1018WS Amsterdam the Netherlands tel. + 31 20 5257089 fax + 31 20 5257064 </div

Normalization Normalization

updated 20.1 years ago • Nataliya Yeremenko

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com

Normalization Normalization

updated 14.5 years ago • Guido Hooiveld

and Ecosystem Dynamics Faculty of Science University of Amsterdam Nieuwe Achtergracht 166 NL-1018WV Amsterdam Netherlands Phone: +31-(0)20-525-6027</div

reposTools reposTools

updated 21.8 years ago • Eneas Aguirre

van Amsterdam Faculty of Science IBED/AMB (Aquatische Microbiologie) Nieuwe Achtergracht 127 NL-1018WS Amsterdam the Netherlands tel. + 31 20 5257089 fax + 31 20 5257064 </div

limma limma

updated 20.1 years ago • Nataliya Yeremenko

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com<http: nutrigene.4t.com

pdInfoBuilder pdInfoBuilder

updated 15.7 years ago • Guido Hooiveld

642-5741<br/>email: <a=20 href='3D"mailto:vranizan@uclink.berkeley.edu"'>vranizan@uclink.berkeley. edu= </a=20></div></body></html> ------=_NextPart_000_00DB_01C26305.03E830D0-- </div

rhdf5 affy rhdf5 affy

updated 23.3 years ago • Karen Vranizan

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com<http: nutrigene.4t.com

updated 15.3 years ago • Guido Hooiveld

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com

updated 11.7 years ago • Guido Hooiveld

did not happen with earlier version 4.0.x, as I remember. Regards, Hongjian hjnwang [at] cmu [dot] edu

edger edgeR

updated 14 months ago • Hongjian

van Amsterdam Faculty of Science IBED/AMB (Aquatische Microbiologie) Nieuwe Achtergracht 127 NL-1018WS Amsterdam the Netherlands </div

arrayMagic arrayMagic

updated 20.2 years ago • Nataliya Yeremenko

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

Pathways Pathways

updated 16.6 years ago • Guido Hooiveld

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

limma limma

updated 15.9 years ago • Guido Hooiveld

lattice" "lqs" "MASS" "methods" "mgcv" [17] "mle" "modreg" "mva" "nlme" "nls" "nnet" "reposTools" "rpart" [25] "spatial" "splines" "stepfun" "survival" "tcltk" "tkWidgets" "tools" "ts" Warning message: package:Biobase

Biobase genefilter tkWidgets Biobase genefilter tkWidgets

updated 22.2 years ago • Scott Norton

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com

GenomicRanges minfi GenomicRanges minfi

updated 13.2 years ago • Guido Hooiveld

lqs MASS methods mgcv modreg mva nlme nls nnet reposTools rpart spatial splines stepfun survival tcltk tools ts Error: couldn't find function "userQuery" In addition

reposTools reposTools

updated 22.6 years ago • Liang-Hao ding

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

Transcription biomaRt Transcription biomaRt

updated 17.1 years ago • Guido Hooiveld

<div class="preformatted">OK. After having used beadarray to get very good results from bead-level data, I've recently read all of the work on the multiple artifact removal methods worked out by the Cambridge group (refs at end of email). Indeed, I may have read them a bit too many times. My question is based on figure 5 from the spatial phenomena paper -- the workflow: http://www.biomed…

Cancer beadarray Cancer beadarray

updated 15.2 years ago • Anand Patel

1.3.5 Biobase 1.4.0 eda 1.8.1 affy 1.3.27 methods 1.8.1 ctest 1.8.1 mva 1.8.1 modreg 1.8.1 nls 1.8.1 ts 1.8.1 base 1.8.1 I also tried R1.9.0-development and Bioconductor development and got the same behavior. I would

hgu133a gcrma hgu133a gcrma

updated 22.0 years ago • Dick Beyer

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com

miRNA microRNA HTqPCR miRNA microRNA HTqPCR

updated 14.4 years ago • Guido Hooiveld

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl<mailto:guido.hooiveld

Annotation biomaRt GenomicFeatures Annotation biomaRt GenomicFeatures

updated 14.8 years ago • Guido Hooiveld

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com<http: nutrigene.4t.com

Pathways Network Pathways Network

updated 15.6 years ago • Guido Hooiveld

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com<http: nutrigene.4t.com

graph Rgraphviz graph Rgraphviz

updated 15.6 years ago • Guido Hooiveld

Read 252162310143_1_of_0004_0635.gpr > > RG1 <- mergeScansRG(RG2,RG1) Error in nls(y ~ .hockey(x = x, alpha1, beta1, beta2, brk), start = list(alpha1 = alpha1, : step factor 0.000488281 reduced below 'minFactor' of 0.000976563

Microarray limma Microarray limma

updated 13.9 years ago • Agnieszka Zmienko

amp; Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com

affxparser affxparser

updated 17.4 years ago • Guido Hooiveld

1000 * | -0.25 #> ------- #> seqinfo: 2 sequences from an unspecified genome nl <- rtracklayer::import(test_bw, which = ranges, as = "NumericList") BiocGenerics::mean(nl) #> [1] -0.937500 -0.500499 sessionInfo() #&gt

Coverage rtracklayer

updated 5.1 years ago • David