Bioconductor Forum

<div class="preformatted">Hello This is a long letter about my efforts of analysis of data in Limma. I have a question about the proper design of my experiment I have 3 groups to compare: A, O, and Y. With 5 A, 8 O, and 7 Y biological samples. I've performed in total 28 two-color microarrays (Agilent 44K) with a mixed number of dye-swaps. My targets file is: HybID fileName sampleID …

Normalization limma a4 Normalization limma a4

updated 20.1 years ago • Nataliya Yeremenko

TRUE, logical = TRUE, warn.conflicts = warn.conflicts, : 'reposTools' is not a valid package -- installed < 2.0.0? > library(reposTools) Error in library(reposTools) : 'reposTools' is not a valid package -- installed

updated 21.2 years ago • Hanif Khalak

command I receive: >Error in library(pkg, character.only = TRUE) : 'test' is not a valid package -- installed < 2.0.0? or, in the second case >Error in library(test) : 'test' is not a valid package -- installed < >2.0.0

updated 20.8 years ago • Giulio Di Giovanni

br/> Error in .testForValidKeys(x, keys, keytype, fks) :<br/>   None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.<br/> > head(t1)<br/> [1] "ENSG00000000003" "ENSG00000000971

annotation

updated 9.1 years ago • z.he

15" "16" "17" "18" "19" "20" "X" # # # # # Check which names need to be changed (need to remove NA's from here --- rest of the scaffolds that aren't chromosome 1-20 or X) # new_chr_names &lt...match # # length(original_chr_names) == length(new_chr_names) # # # # Assign the new chromosome names # names(BSgenome.Mfascicularis.NCBI.6.0@seqinfo) <- new_chr_names # # # Error in `seqnames&am…

BSgenome.Mfascicularis.NCBI.6.0

updated 9 months ago • Genevieve

**12 Doctoral Candidates f/m/d Plant Proteomics, Bioinformatics and Biology** The opportunity: Plants are the nutritional basis of life on earth and protein-rich foods from plants are a global megatrend essential for sustaining an increasing human population and counteracting climate change. However, little is known about crop proteomes – the entirety of proteins that execute and control nearl…

JobPosting

updated 3.8 years ago • mengchen18

Hi there, running Isotope with validation detection in R using the CAMERA package - running it as described in vignette.  I get the following error: <pre

camera metabolomics

updated 7.9 years ago • bhgyu

be listed in more than one probe set, then will the results of the RMA algorithm in affy still be valid? Thanks, Jeff Sorenson</div

cdf probe cdf probe

updated 22.7 years ago • Jeff Sorenson

Dear Bioconductor community, I have time-course Nanostring data and despite having looked at the vignette and several examples I can't figure out how to make the proper design or if I can use Deseq2 at all for my problem. I have 2 groups: Con and Bio, that had blood drawn in 4-time points (0h, 0.5h, 3h, 8h). The problem here is that the Con group has only 2 subjects, whereas the Bio has 3. So…

DESeq2

updated 5.1 years ago • ijvechetti

ENSG00000278704.1 ENSG00000277400.1 ... ENSG00000182484.15_PAR_Y ENSG00000227159.8_PAR_Y rowData names(10): source type ... havana_gene tag colnames(224): GTEX-14LZ3-0011-R10b-SM-6AJA9.1 GTEX-17HII-0011-R10a-SM-79OMY.1 ... GTEX-1GTWX...0011-R10b-SM-CJI2X.1 GTEX-1HCU6-0011-R10a-SM-CKZP8.1 colData names(198): rail_id external_id ... recount_seq_qc.errq BigWigURL #this is the rse detail for a…

DESeq2 recount GTEx TCGA recount3

updated 2.6 years ago • David

distal, ProximalvsRectum = proximal - rectum, DistalvsRectum = distal - rectum, levels=design2) fit2 <- lmFit(MVals, design2) fit2 <- contrasts.fit(fit2, cm2) efit2 <- eBayes(fit2, robust = TRUE) naind <- is.na...rowSums(efit2$p.value)) naind[which(naind=='TRUE')] #named logical(0) ``` Also I have checked that my M-values ma…

DMRcate

updated 4.1 years ago • jfertaj

to produce an DGEExact output table. The data frame contains the log-concentration (i.e. expression level), the log- fold change in expression between the two groups/conditions and the p-value for differential expression as...sequencing data). I would like to know how to write.table this object. If I write.table (object name,"file.txt",sep-"\t",col.names=NA), the error is returned Error in data…

Sequencing edgeR Sequencing edgeR

updated 15.0 years ago • Karen Sherwood

Hi I am trying to get a camera test working after my differential expression in limma. I do not know how to set up camera properly here, because contrast 1,2,3 is not the same as co efficients 1,2,3 in my DE analysis - because the results are not right. I am stuck, any words of wisdom? colnames(design) <- c('class1', 'class2', 'class3', 'age', 'gender') matrix <- data.matrix(da…

limma

updated 9.6 years ago • chris86

server (2 processors) vendor_id : AuthenticAMD cpu family : 15 model : 5 model name : AMD Opteron(tm) Processor 248 stepping : 10 cpu MHz : 2190.480 cache size : 1024 KB fpu : yes fpu_exception : yes cpuid level : 1 flags

updated 18.6 years ago • D.Enrique ESCOBAR ESPINOZA

div class="preformatted">Hi KJ Lim, Once you have your row names of interest i.e up-regulated or down- regulated genes you can easily fetch other information for those row names. For...expVal<-(eset[geneList,]) # Assuming eset if the expression set, it will take all columns for row names matching the geneList >heatmap(expVal) # this will create the heat map In a similar way you …

limma edgeR limma edgeR

updated 13.5 years ago • Ekta Jain

**Postdoctoral Scientist, Proteomics Bioinformatician** **WEHI Proteomics and Mass Spectrometry Facility, Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Melbourne, Australia** **About the position** We are seeking to appoint a highly motivated and experienced statistical bioinformatician with experience in a relevant discipli…

JobPosting Proteomics Statistics Job

updated 5.0 years ago • Laura

<div class="preformatted">Hi All, I am trying to apply Non-Specific Filtering to Affymetrix GeneChip hgu133 plus2 data. Since it has been shown that there are multiple probe sets mapping to the same gene in Affymetrix GeneChips (ref: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1784106/), I thought it is necessary to filter those. So I decided to use nsFilter{geneFilter}. First I preproce…

probe genefilter PROcess probe genefilter PROcess

updated 13.5 years ago • zeynep özkeserli

Hello Bioconductor support: I've searched many other posters but failed to figure out my problem. Here is the introduction to my data. I have eight groups of phenotypes I interested in, which has 7 or 8 biological replicates in each group, and the total number of samples is 55. I've got an unnormalized read cout matrix and a normalized rpkm matrix. The key point is biological replicat…

sva batch effect deseq2 edgeR

updated 8.6 years ago • littlefishes20

P 11 sample_5 after B P 12 sample_6 after A P</pre> The base factor levels are "before", "A" and "N" (in `` df[2:4] ``) after re-levelling. Previously I have combined the factors into various different combinations...If not, how should I formulate them? 1) Which genes are DE after treatment? results(dds, name="time_after_vs_before") Given the other b…

deseq2

updated 8.8 years ago • vincent.knightschrijver

I am running an experiment where we have samples from a number of individuals, pre and post treatment. These individuals were then also grouped according to features found in the DNA. So, overall the design looks like this. I named pre treatment "before" so that DESeq2 will automatically take it as the first level in the factor. All three groups are of interest to compare to the other two (none o…

deseq2

updated 8.2 years ago • hmgeiger

<div class="preformatted"> Hi I have the following samples: batch [1] 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 2055 1802 1802 2055 [16] 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055 1802 1802 [31] 1157 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 2055 2055 [46] 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055 Levels: 1157 1802 2055 treatmen…

updated 12.0 years ago • Guest User

a linear relationship between just 2 "clouds" of data (assume there are many samples for each factor level)? Even if one can clearly distinguish between t and ut - assuming a straight line may wrong. This is like drawing a straight...give wrong results. However, if one just wants to distinguish between t and ut, would the lm be a valid method? I'm reading some "beginners" literature about lm's,…

DOSE DOSE

updated 21.8 years ago • Arne.Muller@aventis.com

I have a microarray data with many duplicated probe names (some are duplicated 2 times, some 10 times, some 35 times). The package limma offers a function avereps() to average expression...across the same probe names, e.g. y.ave <- avereps(y, ID=y$genes$ProbeName). However, I do not want to run lmFit on averaged expression levels. A piece of...duplicate). Is there any option to run lmFit …

limma

updated 8.2 years ago • kgorczak

if you have several conditions for one factor, we address this in Section G of the vignette on multi-level conditions. You just need to specify which level is the base level. Then in the DE analysis, the other two levels will be...then, for three samples with something like colData(dse)$condition <- factor(c("ctrl","A","B"), levels=c("ctrl","A","B")), would be: design(dse) <- ~ 1 …

Clustering GenomicRanges DESeq2 Clustering GenomicRanges DESeq2

updated 12.7 years ago • Michael Love

I have been working on getting the differential expression of proteins for 2 groups - control and treatment. Control has 4 animals while treatment has 5 animals. The samples are collected at the baseline time and after 2 hours. The serum was used to do a somascan assay. I have been using the limma model to get the differential expression of proteins but I am constantly getting an error after I ap…

somascan limma

updated 9 months ago • kkeole1

significant genes that I called “sigG”. Firstly, I used genefilter to find genes that have similar level of expression than my “sigG”.  For each sigGene I got 10 genes which make a background set of 1040 genes (backG). I run topGO...inSelection = geneIDs %in% backG_SxT algSxT <- factor( as.integer( inSelection[inUniverse] ) ) names(algSxT) <- geneIDs[inUniverse] tab …

topGO gene ontolology rnaseq

updated 8.8 years ago • colaneri

problem might be and which package might cause these issues. Error in checkSlotAssignment(object, name, value) : assignment of an object of class "DFrame" is not valid for slot 'elementMetadata' in an object of class "DESeqResults...files <- file.path(dir,"salmon", samples$run, "quant.sf.gz") names(files) <- samples$run tx2gene <- read_csv(file.path(dir, "tx2gene.genco…

DESeq2

updated 4.8 years ago • Anna

nbsp; compute\_NCListAsINTSXP\_length: NCList object is too deep (has more than   100000 levels of nested ranges)__ In addition: Warning messages: 1: In ChIPQC(samples, annotation = "hg19") :   No chromosomes specified...hg19",peaks=NULL,chromosomes="chr11")__ The report change to __Error in checkSlotAssignment(object, name, value) :    assignm…

ChIPQC

updated 8.1 years ago • Victor Goitea

TRUE, single.end=FALSE, param=param) Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a vector type, was 'NULL'</pre> Could someone explain me the error? Does the error come from my reads...Object) 24: initialize(value, ...) 23: initialize(value, ...) 22: new("SummarizedExperiment0", NAMES = names, elementMetadata = rowData, …

summarizeoverlaps GAGE

updated 10.1 years ago • user31888

Hi everyone! Whilst exploring the functions in `` Rsamtools `` and getting familiar with it, I seem to have stumbled upon a potential Bug. I was trying to using the `` ScanBam() `` function to extract part of my bam file while selecting for a optional tag named "B1". For example,  given these example lines from the bam file : <pre> NS500688:47:HG2VTBGXX:1:22304:7555:…

rsamtools bug

updated 8.7 years ago • joelrrv

kallisto output into tximport in order to afterwards use DESeq2 for differential expression at gene level. I just reinstalled R, Bioconductor, tximport, tximportData, as I saw in some of the previous posts this solved the issues...ERX163062 ERR188356 > files <- file.path(dir, "salmon", samples$run, "quant.sf.gz") > names(files) <- paste0("sample", 1:6) > all(…

file.exists false kallisto tximport

updated 3.1 years ago • cta

time + condition:time) colData(DESeq_data)$condition <- factor(colData(DESeq_data)$condition, levels = c("inf", "non")) # Set non-infected as comparing condition DESeq_data$condition <- relevel(DESeq_data$condition, "non") DESeq_data...LRT", reduced = ~condition + time) res48inf <- results(DESeq_data, independentFiltering …

DESeq2

updated 4.1 years ago • nikolaus.virgolini

quantile normalization rownames(lenorm) = rownames(exprs(leukemiasEset)) # add row names colnames(lenorm) = colnames(exprs(leukemiasEset)) # add column names exprs(leukemiasEset) = lenorm # overwrite initial exprs...in% c("CML", "NoL")] cml_normal$LeukemiaType = factor(cml_normal$LeukemiaType) ##set the reference level to be our normal samples: cml_normal$LeukemiaType = relevel(cml…

rowttests

updated 3.9 years ago • leonardorosas2001

lt;- GOGraph("GO:0016265",GOBPPARENTS) > g <- removeNode("all",g) > mt <- match(nodes(g),names(goterms)) > nodattr <- makeNodeAttrs(g,label=paste(nodes(g),goterms[mt],sep="\\\n"), > shape="ellipse",fillcolor="#f2f2f2", > fixedsize...GO:0009605 "response to\\\nexternal stimulus" So the node l…

updated 17.5 years ago • Brian D.Peyser,Ph.D.

e) Error in .C(twins, n, jp, as.double(x2), dv, dis = double(if (C.keep.diss) length(dv) else 1), : 'name' must be a string (of length 1) or native symbol reference Could anyone point me to the right direction on to how to fix this

Microarray GO Clustering adSplit Microarray GO Clustering adSplit

updated 13.6 years ago • Luz Mayela Soto

updateObject(toll10b_k27ac_2to4h_1.ranges, verbose=TRUE) updateObject(object = 'GRanges') Error in names(ans) <- seqnames(x) : 'names' attribute [12] must be the same length as the vector [0]</pre> I can provide a download link for the saved

genomicranges

updated 11.1 years ago • Jeff Johnston

SYMBOL... > Error: 2 errors; first error: > Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), : 'data' must be of a > vector type, was 'NULL' I am wondering if this issue is related to an error to the GEOquery

Preprocessing hgu95av2 virtualArray Preprocessing hgu95av2 virtualArray

updated 11.6 years ago • Guest User

the argument 'x' in selecting a method for function 'head': Error in rowRanges(vcf) : Argument 'x' must be a matrix or a vector. or even empty outputs, such as:  geno(vcf) List of length 0 names(0):  > sapply(geno(vcf), class) named

variantannotation readvcf

updated 10.5 years ago • pifferdavide

<div class="preformatted">Hi Sneha, sneha patil wrote: > hii, > Myself Sneha.... > *I am creating own chip CDF and probe package file with a window R > *2.0.1 >> * version. > *>* > *>* The make.cdf.package works fine, > *>* > *make.cdf.package("HuGene-1_0-st-v1.r3.cdf", species = "Homosapiens_sp") &a…

cdf probe cdf probe

updated 15.9 years ago • James W. MacDonald

<div class="preformatted">Dear Tiandao, There is no good way to plot residuals for microarray experiments that I know of, so I am not at all sure what you have in mind here. You cannot sensibly do one big plot of all the residuals because the data is so heteroscedastic across genes, as well as being dependent. The residuals() method for MArrayLM objects doesn't work when ndups>1. D…

Microarray limma Microarray limma

updated 18.2 years ago • Gordon Smyth

new("NgsTilingPDInfoPkgSeed", ndfFile = ndf, xysFile = xys, posFile = pos, author = "Name", email = "email", biocViews = "AnnotationData", genomebuild = "unspecified", organism = "unspecified", species = "unspecified") makePdInfoPackage...0 rows into table bgfeature... Error in sqliteSendQuery(con, statement, bind.data) : bind.data must…

microarray R oligo micro array data annotation

updated 10.3 years ago • zenekzkk

fold change ratio to define differentially expressed genes (DEGs) identified by DESeq2. Would it be valid to submit a manuscript where the DEGs are identified only with a padj threshold? Many thanks for the opinion on this

deseq2

updated 5.3 years ago • marija.buljan.2

run the same ML exercise and compare results. This works fine, but my questions is: Is this is a valid approach to subsetting the data frame because the VST counts have been generated with ALL the data and therefore variance...stabilising considers ALL samples. Or is a more valid approach to subset the DESeq2 object by age 1 and 2 and by age 3,4,5,6 -- and generate VST counts individually?…

deseq2 rna-seq

updated 5.6 years ago • A

Once the file has been processed by ArrayExpress, and the header removed, the file is no longer a valid GPR format file. You therefore use format="generic" and supply the column names, just as you've done. I expect what you give...by arrayexpress which > looked something like this: > > > > SlideNumber Source > Name Label FileName > 1 8CT…

limma ArrayExpress limma ArrayExpress

updated 16.5 years ago • Gordon Smyth

that was added above cd <- as.data.frame(colData(rse_gene)) View(cd) #confirm that row names in the colData (cd) matches the column names in cts (the assay of the data) all(colnames(cts) %in% rownames(cd)) #TRUE #confirm they...make the dds dds <- DESeqDataSet(rse_gene, design = ~condition) #set the factor level #compare the other levels to the untreated sample dds$…

DESeq2 heatmaps

updated 2.8 years ago • m-bihie

<div class="preformatted">Dear all, I am trying to write the R code for the analysis of a microarray experiment involving both technical replication and common reference design. The targets file is: --------------------------------------------------------------------- FileName Cy3 Cy5 Array1A.gpr Ref1 WT1 Array1B.gpr Ref1 WT1 Array2A.gpr Ref2 WT2 Array2B.gpr Ref…

limma limma

updated 18.1 years ago • Juan C Oliveros Collazos

contrast=c("treatment",'treated',"control"))</pre> Here I assume that DESeq2 treats B16 as a base level of `` cell_line ``. For the second cell line I do:   `` TC1A9.result <- results(dds, list( c("treatment_ifng_vs_control","cell_lineTC1A9.treatmentifng...metadat$cell_line,'_',metadat$treatment)) metadat_collapsed$condition <- factor(dds$condition, levels = c("unt…

deseq2 apeglm

updated 7.0 years ago • zolotaryovgl

The tumors correspond to 2 cell lines and have either Low or high intensity: <pre> Sample name Intensity CellLine 1 CDX_1_1 Low_BLI CDX_1 2 CDX_1_2 Low_BLI CDX_1 3 CDX_2_1 High_BLI CDX_2 4 CDX_2_2 High_BLI CDX_2...modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified. Levels or combinations of levels without any samples hav…

deseq2 multiple factor design

updated 8.3 years ago • Jane Merlevede

chromosome="chr5", genome="hg19", >>rstart="exonStarts", rends="exonEnds", gene="name", symbol="name2", >>transcript="name", strand="strand", name="RefSeq Genes", feature="name2", >>showId=T, from=122428653, to=122432628...to=122432628) >>Error in unit(rep(1, n), "strwidth", data = data) : >> 'x' and 'units' must have length &…

updated 13.3 years ago • florian.hahne@novartis.com

<div class="preformatted">Since this becomes a fairly large thread that goes in many different (and interesting) directions, I propose to start a new one with a more explicit title. I will try to summarize major points discussed so far. - Thomas Friedrichsmeier [Thomas.Friedrichsmeier@ruhr-uni-bochum.de] after "having a short conversation with the obveRsive-people" introduced the idea of …

graph graph

updated 23.0 years ago • Philippe Grosjean

RG$G, method="quantile") RG$G <- log2(RG$G) f <- factor(targets$Condition, levels = unique(targets$Condition)) design <- model.matrix(~0 + f) colnames(design) <- levels(f) fit <- lmFit(RG$G,design) contrast.matrix...lt;- makeContrasts("Condition1-Condition2",levels=design) fit2 <- contrasts.fit(fit,contrast.matrix) fit2 <- eBayes(fit2) topTable(fit…

GO probe limma GO probe limma

updated 16.5 years ago • Marcel Dinger

something like <pre> patient<-factor(samples$Patient) fraction <- factor(samples$Fraction, levels=c("CellType1, "CellType2", "CellType3", "CellType4"))</pre> <pre> 1. design <- model.matrix(~patient+fraction) fit <- lmfit(exprsset...fractionCellType3, fractionCellType1 - fractionCelltype4, <em>(all other pairwise comparisons)</em>, …

microarray limma design and contrast matrix

updated 8.7 years ago • Anna

<div class="preformatted">The question of what is appropriate biological replication is a tough one. The objective is to obtain results that are valid in the population of interest, which usually is not plants grown in a single batch in the green house. But how much variability should we induce? Each batch of plants grown separately but in the same building (different growth chambers), g…

Normalization probe affy affyPLM Normalization probe affy affyPLM

updated 19.9 years ago • Naomi Altman

bioconductor I am posting a bug report here. The problem is import function calls parseURI on file names: <pre> library(rtracklayer) import.bed("my bed file.bed") <span style="background-color:Yellow">Error in parseURI(uri) : cannot

software error rtracklayer

updated 10.3 years ago • balwierz

at the low end (see graph). Is this due to the t-statistic being based on a higher df? If so is this valid as the biological information hasn't changed? If I now compare to my affy data then I get a similar situation (ie: less significant...fit <- eBayes(fit) -------------- next part -------------- A non-text attachment was scrubbed... Name: dupCor.png Type: image/png Size: 17921 bytes D…

affy limma oligo affy limma oligo

updated 21.1 years ago • Matthew Hannah

443': - The certificate is not issued by a trusted authority. Use the fingerprint to validate the certificate manually! Certificate information: - Hostname: *.fhcrc.org - Valid: from Sat, 18 Oct 2014 16:52:00 GMT until...443': - The certificate is not issued by a trusted authority. Use the fingerprint to validate the certificate manually! Certificate information: …

software error github

updated 9.3 years ago • emathe

Annotation : aPleWal.anno.v2.20220926.gtf (GTF) Dir for temp files : ./ Threads : 10 Level : meta-feature level Paired-end : yes Multimapping reads : not counted Multi-overlapping reads : not counted Min overlapping...manual…

Subread GTF featureCounts segmentationfault

updated 2.8 years ago • yao hua

Hi Lima and DESeq2 community, I'm trying to study treatment effects on two different __Phenotypes__ (say, Disease and WT). 7 patients were collected for the Disease group while 6 normal people were collected for WT. For each of these 13 subjects, RNA-seq data were generated after 3 different __Treatments__ which were a Vehicle control, a Drug A treatment and a Drug B treatment. From the PCA plo…

limma deseq2

updated 9.6 years ago • dustar1986

data (not image files) obtained from affymetrix chip and I used limma to analyze it.  The row names of top table does not match the probe id. I saw this thread for annotating results from celfiles (https://support.bioconductor.org...Code: dat<-read.csv("Rat\_Gene\_Expression\_Array.csv")   \#\#\# importing data  names(dat) Heart\_dat<-dat\[c("Pr…

limma annotation

updated 10.7 years ago • kaushal Raj Chaudhary

the package Rgraphviz but I have the following message error: configure: error: please specify a valid path to 'dotneato-config' version >= 1.12 using --with-graphviz=DIR What do I have to do?? Caroline bernard-michel</div

Rgraphviz Rgraphviz

updated 20.7 years ago • bernard-michel caroline