Bioconductor Forum

For full disclosure I posted this question on the Phyloseq Github page but perhaps this forum is more appropriate. I have a 16S dataset from gut mucosa and want to analyse differential abundance according to a factor. I have 200 samples: 10 cases and 190 controls. Q1: is it valid to use DESeq2 to compare differential abundance with DESeq2 with such an a large imbalance between the numbers o…

deseq2

updated 6.5 years ago • dr.aj.scott

be very grateful for help. Best wishes, Magdalena homedir="D:/TCGA Methylation Analysis/DATA/KIRC/LEVEL 1/Pairs_HumanMethylation27" dirs=list.files(homedir) batchNames=gsub("jhu-usc.edu_KIRC.HumanMethylation27.","",dirs...homedir,dirs[i]) fns=files[[i]] for(j in seq(along=fns)){ cat(".") ###Get the sample name tmp=strsplit(readLines(file.path(tmpPath,fns[j]),n=1),"\t") cnames[ j+st…

updated 14.0 years ago • Magdalena Wozniak

<div class="preformatted"> Hi, I'm having the same problem as the person in the post below, namely, a call to qc() fails with the message "Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: xyzcdf", even though...<div class="preformatted"> Hi, I'm having the same problem as the person in the post below, namely, a call to qc() fails with the message "Erro…

GO cdf probe gcrma simpleaffy affyQCReport GO cdf probe gcrma simpleaffy affyQCReport

updated 19.6 years ago • Wittner, Ben

x[,1]) >=1 & x[,2] < 0.05)} > diffgenes<-selectFUN(input) > myInterestedGenes<-names(which(diffgenes==T)) > geneNames<-rownames(input) > geneList<-factor(as.integer(geneNames %in% myInterestedGenes...gt; names(geneList)<-geneNames > str(geneList) Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ... - attr…

GO GO

updated 16.3 years ago • Scott Ochsner

I am trying to add a contrasts matrix to a analysis to compare the average of the means of two groups in the primary factor of interest.  Just to make things interesting my design matrix has a bunch of unnamed latent variables churned out by SVA.  I have noticed one annoying issue could be called a bug, is that all the manuals seem to specify contrasts.fit with out explicitly na…

limma

updated 11.1 years ago • kodream

from GOstats. I get the following error: Error in initialize(value, ...) :    invalid names for slots of class “GOHyperGResult”: pvalues, oddsRatios, expectedCounts, catToGeneId, organism Here the code I use: <pre

gostats

updated 8.0 years ago • laianavarromartin

least non-significant no? The code is rather straightforward: ``` baseMeanPerLvl <- sapply( levels(dds_sub$CellType), function(lvl) rowMeans(counts(dds_sub,normalized=TRUE)[,dds_sub$CellType == lvl, drop=F] ) ) resultsNames...dds_sub) res1<-results(dds_sub,name = "CellType_Neutrophils_vs_Eosinophil", alpha = 0.05) res1<-lfcShrink(dds_sub,coef = "CellType_…

DESeq2

updated 2.4 years ago • andrebolerbarros

a number of multiple comparison procedures. Is it reasonable to average probe set expression levels for the same gene? Are there any "pre-processing" routines that address this issue? The flip side of this question is "Do...same gene symbol really specify the same gene? Does it matter which annotational method is used to name genes?" </div

hu6800 probe hu6800 probe

updated 20.3 years ago • jsv@stat.ohio-state.edu

possible to do it, with default options (and I would like to do that with 1500 genes or so...). Gene names (and branchs too) collapse together... I tried, setting new device dimensions (jpeg() or png() height and width), and modifying...fin, etc..), to have long cluster figures (to be clear, dChip style). Well, it works for others high-level graphical functions, but it doesn't work for heatmaps(…

Clustering Clustering

updated 21.1 years ago • Giulio Di Giovanni

keep getting an error message saying: <pre> (data, reference, dnn = dnn, ...) : all arguments must have the same length</pre> I assume this must be in relation to my list of markers, but am unsure why this is occurring. I have...is the marker list.  <pre> w <- table(fData(msnsetmarkers)[, "markers"]) w <- 1/w[names(w) != "unknown"] # the part I g…

bioconductor proloc

updated 7.7 years ago • sjp221

I want to use the satuRn package to test for differential transcript usage between two diets. My data is in the sumExp. I set up the contrast matrix L and try to run the satuRn::testDTU function as described in the vignette. I keep on running into the same error and dont unterstand fully where it comes from. Does someone have experience with that can can help? Thank you so much ```r #1. Co…

SummarizedExperiment satuRn

updated 16 months ago • Marcus

I am comparing each mutant clone to the WT. pData_1$condition <- factor(pData_1$condition, levels = c("WT", "C3", "C6","C10")) I include the batch information in my design: pData_1$condition <- relevel(pData_1$condition, ref = "WT") # set...contr.treatment" attr(,"contrasts")$condition [1] "contr.treatment" The…

DESeq2 BatchEffect

updated 3.2 years ago • annamariabugaj

Hello, I am analyzing an RNA-seq dataset generated by a previous lab member and I have a question regarding DESeq design for a time-series analysis. The data was generated from a drug treatment performed in vitro (same cell line for all samples) and I have the following samples to work with: 0h - No treatment, a single set of duplicate samples collected 2 days - duplicates collected for dr…

RNASeq DESeq2 timecourse

updated 23 months ago • WS

value by the sum of : - a constant term (maybe null actually) - a gene effect : approximately 6000 levels - a fraction effect : 3 levels - a medium effect : 2 levels - a rep effect : 2 levels for each medium - and possibly all two-order interactions...phi.outliers] : non-conformable arguments > traceback() 4: which(cdf@name == i, arr.ind = TRUE) 3: locate…

GO Yeast cdf genefilter affy PROcess GO Yeast cdf genefilter affy PROcess

updated 23.6 years ago • julien.sylvestre@wotan.ens.fr

models I now have, which one is theoretically better to use? The one with the most genes, most level detectors, or most features (domains)? Or the one with the lowest average prediction error, disregarding all other factors...components to build the model: > > (server) > genes: 4055 of 5667 > features: 3553 > level detectors: 74 > > (home) >…

Genetics Coverage biomaRt gene2pathway Genetics Coverage biomaRt gene2pathway

updated 15.3 years ago • Bogdan

I use an additive model?__ I guess that to determine the appropriate test for association, we must first specify a genetic model. Currently, it is quite established in the scientific community that an additive model...cond<-c(cond,u)   pairs\_edge\[\[counter\]\]<-cond   counter<-counter+1 } names\_edge<-names(table(design$Condition)) if(…

deseq2 edger differential gene expression additive model

updated 9.9 years ago • jlerga

written for it and to be precise, the particular Tcl/Tk packages that are called by R packages must be installed into Tcl/Tk on your computer. Tcl/Tk packages maybe installed in /usr/lib or /usr/local/lib. For eg. On my Linux...X11. ===================== If an R package is going to use Tcl/Tk then the interface package tcltk must be installed into R. (It is installed with a standard install of R…

limmaGUI affylmGUI

updated 15 months ago • Keith Satterley

<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 15.1 years ago • Anand Patel

ENSG00000000003 ENSG00000000005 ...<br/>   ENSG00000281912 ENSG00000281920<br/> rowData names(3): ensembl_gene_id external_gene_name<br/>   original_ensembl_gene_id<br/> colnames(521): TCGA-3L-AA1B-01A-11R-A37K...11R-A155-07 ...<br/>   TCGA-AA-3675-01A-02R-0905-07 TCGA-G4-6323-01A-11R-1723-07<br/> colData names(101): sample pati…

tcgabiolinks rnaseq normalization EDASeq

updated 8.0 years ago • svlachavas

an error that the header files cannot be found. After consulting the read_me, I concluded that it must be that ChemmineOB cannot find the open babel files. So I set out to specify the correct paths using: `R CMD INSTALL --configure...cannot be found. Unfortunately this babelconfig.h file is in a different (although closely named) directory: openbabel-openbabel-2-4-0/build/include/. (notice i…

ChemmineOB Linux Installation

updated 6.7 years ago • jandrosavich

like manner, for which the model expressed in R formula is `~x*z`, where `x` is a factor of two levels `"a"` and `"b"`, and `z` is a factor of three levels `"a"`, `"b"`, and `"c"`. And I would like to do a LR test for all the interaction terms at once. The...design matrix, say from `model.matrix` would have columns named `"(Intercept)"`, `"xb"`, `"zb"`, `"zc"`, `"xb:zb"` and `"xb:zc"`, the inter…

MAST

updated 2.8 years ago • Ken C

Hi, We recently received a dataset of 48 rat samples on 6 Agilent G3 GEx Rat V2 chips. I have no experience with Agilent arrays so I’m really struggling with this one. A couple of questions I was hoping someone could help me with: 1) This dataset contains samples from 3 different tissues that were randomized across all chips. I was wondering whether it is ok to read in all the data in at once …

Agilent limma

updated 4.4 years ago • AB

seeks applications for a faculty position. Appointment is at the Assistant or Associate Professor level and in either the Adjunct or In Residence series. Duties: Pursue an independent bioinformatics research program and...ranging from proposal development through data analyses. Provide bioinformatics instruction at all levels. Qualifications: Ph.D. in bioinformatics, statistics, biostatistics, …

Microarray Microarray

updated 16.8 years ago • mark@biostat.ucsf.edu

<div class="preformatted"> Hi Could someone please help me out with this error on a hyperGTest with KEGG parameters? I get the same error on the hgu133plus2 chip. Must be something wrong with my parameter definition but I can't work out what. > params<-new("KEGGHyperGParams", geneIds =entrez_set0.05...with this error on a hyperGTest with KEGG parameters? I get the same error…

Annotation GO hgu133plus2 moe430b mouse4302 Annotation GO hgu133plus2 moe430b mouse4302

updated 16.6 years ago • John Coulthard

<div class="preformatted">Hi all, I'm struggling with the meta-analysis of microarray data. In the user guide of the bioconductor package "MAMA" there is an exemple of meta- analysis in cancer microarray data concerning the comparison of expression profiles in MSI (microsatelite instable) and MSS (microsatelite stable) colon cancer. Data are gathered from three microarray experiments from …

Microarray Cancer Colon limma Microarray Cancer Colon limma

updated 14.4 years ago • Manuela Di Russo

LP", chip = "org.Hs.eg.db") Error in .get_eg_to_go_fun(mapfun, chip) : either mapfun or chip must be specified In addition: Warning message: object 'org.Hs.egGO2PROBE' not found DB-based version of org.Hs.eg.db not...LP", chip = "hgu133plus2.db") NA</pre> The argument description says: <pre> chip The name of a DB-based annotation data package (the name will end in …

gostats

updated 9.3 years ago • Lluís Revilla Sancho

chr [1:17] "cond07.rep0020" "cond07.rep0021" "cond07.rep0022" "cond08.rep0023" ... .. ..$ : Named logi [1:6351] FALSE FALSE FALSE FALSE FALSE FALSE ... .. .. ..- attr(*, "names")= chr [1:6351] "38536" "38537" "38538" "38539" ... > > # estimate dispersion...chr [1:17] "cond07.rep0020" "cond07.rep0021" "cond07.rep0022" "cond08.rep0023" ... .. ..$ : Named logi [1:6351] FALSE FAL…

Normalization edgeR Normalization edgeR

updated 14.2 years ago • Nick Schurch

In the RNA-Seq workflow: gene-level exploratory analysis and differential expression   source('http://www.bioconductor.org/help/workflows/rnaseqGene

rnaseqgene genomicalignments

updated 10.5 years ago • hope-dream

step, checkFunc = function(...) TRUE){ n <- length(obj) if(width < 1){stop("Window width must be ≥ 1.")} if(step < 1){stop("step must be ≥ 1.")} if(any(width > n)){stop("The window size cannot be greater than number of data elements.")} state...lt;- new.env() state$i <- 0L state$obj <- obj if(is.null(ref)){ state$ref &…

dnastringset parallel iterators

updated 10.0 years ago • ben.ward

not only to supply Sample_platform_id, but also a "Sample_platform_title" which would contain the name of the chip as given by the manufacturer. 3, Sample descriptions: Since most data are useless w/o the sample description...GSExxxx # gse: GEOqueryclass imported from GEO GSE file GSExxxx_family.soft (or soft.gz) # column: name of column to be extracted from data table # load libraries l…

hgu95a hgu95av2 GEOquery hgu95a hgu95av2 GEOquery

updated 19.9 years ago • Christian.Stratowa@vie.boehringer-ingel…

description, 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...DFG analysis design <- model.matrix(~0+factor(group_list)) colnames(design) <- levels(factor(group_list)) r…

GEOquery ArrayExpress limma DifferentialExpression

updated 19 months ago • SSSJec

Hi, I have a GRanges object "__MB\_granges__" which has data from __Chr1 - Chr22,__ also __ChrX__ and __ChrY.__ I had removed __ChrX__ and __ChrY__ using the following command.  <pre> > <strong>seqnames(MB_granges)</strong> factor-Rle of length 485512 with 24 runs Lengths: 46857 34810 25159 20464 24327 36611 30017 20950 9861 24388 ... 21969 27879 5922 25…

GRanges subsetting

updated 7.3 years ago • lalchungnungabt17

class="preformatted">Hi folks, I'm analyzing microRNA data using limma and I'm wondering about the validity of the p-values I'm getting out. Its a simple 'Group A Vs Group B' experimental design. 4 arrays in one group, 3 in the other...the multiple test hit. Can anybody explain why limma is giving me such lower values and if they are valid? I can provide more information if required. Thanks,…

miRNA limma microRNA miRNA limma microRNA

updated 16.1 years ago • Paul Geeleher

I'm reading the data from an excel sheet and create an object for each time point and treatment level. > data_1.0 <- read.delim(file="stress_1.0.txt", row.names=1) > dim(data_1.0) 22810 51 I than combined the various time...the treated and the control experiments. > targets <-readTargets("targets.txt",row.names="Name",quote="") > lev <- c("wt…

updated 16.6 years ago • Assa Yeroslaviz

<div class="preformatted">Hi Michael, On 7/8/2011 1:36 PM, Michael Bauer wrote: > I'm one of the system administrators at Heather's site. I have a message > to the list languishing in the moderation queue, which asks the simple > question: given R, Bioconductor, the data set, and that error message, > how do I extract what additional package(s) it needs to insta…

Microarray Annotation cdf probe cycle Microarray Annotation cdf probe cycle

updated 14.4 years ago • James W. MacDonald

online and when I download database) and in hgu133plus2.db, I can't see them associated with gene names.   For instance, I can use two methods to get gene names: <pre> biocLite(hgu133plus2.db) biocLite(annotate) r=rownames

Annotation hgu133plus2

updated 8.8 years ago • benoit.tessoulin

Documents/Prosjekter/RNA- project/Data/Sycon_ciliatum/sycon-from-Bergen/gff-files-and- expression-levels/cds.gb.gff3", + format = "gff") extracting transcript information Extracting gene IDs extracting transcript information...Exon Rankings. If this is not what you expected, then please be sure that you have provided a valid attribute for exonRankAttributeName Error in unlist(mapply(.assignRanki…

Genetics TranscriptDb GenomicFeatures

updated 11.3 years ago • Jon Bråte

each). VCFfiles are generated using GATK. I would like to know what is the heterozygosity levels for each samples. I readVcf files and created snpmat using MatrixToSnpMatrix. tab <- TabixFile("./Allsamples_gatk.q_50_30.vcf.gz...2012 at 2:50 PM, Yadav Sapkota <ysapkota@ualberta.ca> wrote: > Hello, > > I am trying to validate few LOH regions using SNP genotype d…

SNP snpMatrix SNP snpMatrix

updated 13.4 years ago • gowtham

treatments) Subject <- factor(targets$subjectids) Treat <- factor(targets$treatments, levels=c("C","T")) design <- model.matrix(~ Subject + Treat) data_mat=dcast(data, gene~ new_sample_name, value.var = "raw_count") y <- DGEList...are not any where close to being the same: ![comparison of p-values tidybulk_edgeR vs edgeR ][4] I must be misunderstanding how to corr…

edgeR R tidyverse tidybulk

updated 3.1 years ago • Amit Indap

Hello All, For my analysis I have three time points Time1, Time2 and Time3 these were measured based upon three different treatments. I am trying to run differential analysis between T1 vs T2, T1 vs T3 and T2 vs T3, I have some technical replicates that I summed using the collapseReplicates() function, the "runsCollapsed" column below describes that. For running the comparison I have tried usin…

RNA rnaseq deseq2

updated 8.3 years ago • hrishi27n

the condition has length > 1 and only the first element will be used in: if (is.na(y)) y else names(y) I'm somewhat unfamiliar with R and I'm entirely in the dark as to what's causing the problem. One person suggested that...lt;- quantile(c(s1means, s2means), probs = seq(0, 1, 0.1)) s1class <- cut(s1means, deciles) names(s1class) <- names(s1means) s2class <- cut(s2mea…

updated 22.4 years ago • Chris Doucette

I have a dataset with 3-factor levels (A, B, C). If I use the data of A, B, C to perform a pairwise comparison between A and B, I got a result very different from that when...drop=F] count_table = count_table[rowSums(count_table) > 0, ] design = as.formula(sprintf('~%s', names(sample_table)[[2]])) suppressWarnings(suppressPackageStartupMessages(library(DESeq2))) cds = suppressWarning…

deseq2

updated 5.7 years ago • megapode32559

lt;- stringr::word(sf_files, -2, sep ="/") coldata <- data.frame(files = sf_files, names = sample_names) ``` This looked like it all worked, but here's the last bit of input and the error messages... ``` > txi_data <- tximeta...and has been removed 3: In prefixColumns(x, columns, clean, with.tables) : The submitted table names are not val…

tximeta SummarizedExperiment DESeq2

updated 4.1 years ago • alex.weiss

aimed at characterising the genetic contribution to immune-mediated diseases. The candidate must have knowledge in human genetics and demonstrated experience with the analysis of large "omics" data (ideally including...genotyping data), as well as good statistical knowledge and strong programming skills. They must have a creative approach to problem-solving, as well as demonstrate excellent ti…

molecularQTL computationalbiology immunology GWAS biostatistics

updated 3.7 years ago • helene.ruffieux

time I try to use qvalue I get the error : "ERROR: The estimated pi0 <= 0. Check that you have valid p-values or use a different range of lambda." I have repeated my limma analysis and end up with the same results. The p values...Error in pi0est(p, ...) :   ERROR: The estimated pi0 <= 0. Check that you have valid p-values or use a different range of lambda. > …

qvalue usage qvalue

updated 10.1 years ago • robandclara

pre> [preprocessQuantile] Mapping to genome. Error in `assayDataElement<-`(`*tmp*`, "Meth", validate = FALSE, value = c(471, : unused argument (validate = FALSE) In addition: Warning message: display list redraw incomplete </pre

illuminahumanmethylationepicanno.ilmn10b.hg19 illuminahumanmethylationepicmanifest minfi limma 850k

updated 8.7 years ago • ceciliebucher

status was `404 Not Found' Note: http://www.bioconductor.org/CRANrepository does not seem to have a valid repository, skipping Warning message: Failed to read replisting at http://www.bioconductor.org/CRANrepository in...Forbidden' Note: http://www.bioconductor.org/repository/devel/package/Source does not seem to have a valid repository, skipping Warning messages: 1: Failed to read replisting at …

cdf affy cdf affy

updated 18.2 years ago • Wei Wang

Hi, I am using Deseq2 to do comparisons between regions of tissue. I have set one region as the the "control" region - BLE. I am trying to pull out the pairwise comparisons for the region named BJK which is third in the factor list. I can run results with contrast for "BLE" vs "BJK" fine but when I try to run results for "BJK" vs "PEK" I run into an error: non-conformable arguments. All …

DESeq2

updated 2.0 years ago • claire

a set of GSM files downloaded from GEO. In addition to providing a table with probe ids, expression levels and p values, I would like to have the ensembl ids associated with the probe ids. I loaded in the corresponding platform...data.frame(exprs(eset_rma), assayDataElement(eset_pma, "se.exprs")) my_frame <- my_frame[, sort(names(my_frame))] write.table(my_frame, file="export.tsv", sep="\…

GO probe affy GO probe affy

updated 13.1 years ago • Guest User

of the same condition) and I do not want to make the assumption that genes with similar expression levels have similar dispersion values. This is why I am interested in getting the dispersion values before fitting/shrinking...towards the curve. I have several questions: I see there is a column named dispGeneEst in mcols(dds). 1. Are the values in the dispGeneEst column the dispersio…

DESeq2

updated 4.8 years ago • raya.fai

proteins. Positive and negative controls are common and spiked into each sample. I have the row names for those. I have run through calculating the logFC between sample groups, but this isn't what I actually want. What I want...sample groups. I think what I want to do is use the sample groupings to predict the protein-level dispersion, and then somehow either introduce a ratio to control int…

edgeR DifferentialExpression

updated 5.1 years ago • anisotropy

of class "Spectrum2" Precursor: 808.5253 Retention time: 0:8 Charge: 2 MSn level: 2 Peaks count: 462 Total ion count: 1423873 For retention time, this worked: head(rtime(rawdata)) #got exact retention time...ion m/z, I don't get an index as an answer. > which(precursorMz(rawdata)==808.5253) named integer(0) Why doesn't this …

MSnbase

updated 6.5 years ago • garfield320

Hi All, When I try to download GSE49656 with GEOquery, errors were always reported: such as __not all columns named in 'colClasses' exist__   When I change to server (linux), some other error reported: __Error in read.table(con, sep = "\\t", header...I try to download GSE49656 with GEOquery, errors were always reported: such as __not all columns named in 'colClasses' exist__ &nb…

GEOquery

updated 9.0 years ago • Shicheng Guo

disease_nos-disease_leimyo, disease_nos-disease_lipo, levels=design) Voom <- voom(RNA_data, design, plot = FALSE,normalize.method = "quantile") vfit <- lmFit(Voom, design) vfit <- contrasts.fit...deg <- topTable(efit, coef = 1,adjust.method = 'fdr', number=Inf) gene_list = deg$logFC names(gene_list) = deg$…

GSEA voom limma

updated 2.4 years ago • manuelsokolov

nbsp;              'source\_name','study\_external\_id','go\_id','name\_1006','definition\_1006', +                                    'go\_linkage..._db\_name, status,tra…

biomart

updated 7.0 years ago • Bioinformatics

knowledgeable in biochem but with mRNA c.2% total RNA, then a 2% change in rRNA and tRNA levels seems more likely than a 100% change in mRNA. Why not just measure mRNA/total RNA in the original sample (I assume there...have standardised to house-keeping genes. Perhaps I'm being naive but could standardising to mRNA level be as valid as the alternatives (assuming you can't use per cell), it obvio…

Microarray Normalization affy limma gcrma Microarray Normalization affy limma gcrma

updated 21.2 years ago • Matthew Hannah

the results of unit testing. I use the following in my ~/.Makefile to see these results imidiately NAME := $(shell basename $(PWD)) # Get current map name Rcheck: # Check R package of current map (cd ..; \ R CMD check $(NAME) && \ if [ -d $(NAME)/inst/unitTests...then \ cat $(NAME).Rcheck/tests/doRUnit.Rout; \ fi) Then only the followin…

graph graph

updated 19.3 years ago • Gorjanc Gregor

pheno parameter contains more than 2 phenotypes, and you want to use ProbeLasso function, you MUST specify compare.group=c("A","B"). Bumphunter and DMRcate should not be influenced. [ Section 1: Check Input Pheno Start ] You pheno...No rownamematches. 'rownames' need to match IlluminaHumanMethylation450k probe names. The same error happens when arraytype="EPIC"…

ChAMP

updated 11 months ago • André

lt;-rma(howard1.raw) I get the following errormessage: Error in hist.default(howard1.norm) : `x' must be numeric Jim MacDonald pointed out to me that a file made with the command > dat1 <- normalize.AffyBatch.quantiles...Isaac Friedman, age 14 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1732 bytes De…

Cancer Cancer

updated 21.6 years ago • Richard Friedman

<div class="preformatted"> >But when I try the widget option I still get: > >> alldata <- ReadAffy(widget=TRUE) >Error in structure(.External("dotTcl", ..., PACKAGE = "tcltk"), class = >"tclObj") : > [tcl] ambiguous option "-col": must be -column, -columnspan, >-in, -ipadx, -ipady, -padx, -pady, -row, -rowspan, or -sticky…

Cancer tkWidgets Cancer tkWidgets

updated 22.5 years ago • John Zhang