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Biobase biomarker neuroscience biotech

updated 5.1 years ago • sandmann.t

Hello, I'm trying to install the IsotopicLabelling package in RStudio using: ``` library(devtools) install_github("RuggeroFerrazza/IsotopicLabelling", build_vignettes = TRUE) ``` The installation requires to loading of the mzR package. I get the following error message during the install: ``` Error: package or namespace load failed for 'mzR': .onLoad failed in loadNamespace() for 'mzR…

mzR IsotopicLabelling

updated 5.2 years ago • holly.douglas

hi, I remember using the ENZYME2AFFY Package before 6 to 8 months now i have downloaded the new version of R and i dont see that package at all what happened to that package. I need that package to find the EC numbers of the

affy affy

updated 22.1 years ago • arun kumar vinnakota

<div class="preformatted">Hello everybody I want to manually up-regulate some genes (a have a list of genes) as compare to other in my normalized gene expression matrix . i am doing this just by increasing the values. I am not sure what number i add in the intensity value of my gene of interest,so that it become up regulated in my normalized gene expression matrix...gene expression matrix …

updated 13.8 years ago • Reema Singh

The download script/function getBioC() is failing for windows. it either needs altering so that version numbers are included eg doing this by hand works Browse[1]> sourceUrl [1] "http://www.bioconductor.org/packages/release

Biobase Biobase

updated 23.3 years ago • Ashley Ford

Read US83000164_251485049983_S01_GE1_105_Dec08_1_3.txt Error in RG[[a]][, i] <- obj[, columns[[a]]] : number of items to replace is not a multiple of replacement length [[alternative HTML version deleted]] </div

updated 16.0 years ago • neeraj rana

can do this to extract all chip results from a specific tissue: exprs(obj)[,which(pData(obj)[,2<or number="" whatever="">]=="liver")] I wonder if there is a way to get all samples from patients with paired samples? I understand this can...but I think it will be so helpful if I can just do this in R. Best Hao [[alternative HTML version deleted]]</or></div

Cancer Cancer

updated 21.7 years ago • Hao Liu

Dear Bioconductor community, i would like to adress a specific problem i encountered after using the package __NbClust__, for getting the optimal number of clusters concerning various measures, regarding a microarray dataset. Although the problem is possibly more generally...adress a specific problem i encountered after using the package __NbClust__, for getting the optimal number of clusters co…

NbClust clustering looping list object function creation

updated 8.7 years ago • svlachavas

gt; packageDescription("Biobase") Package: Biobase Title: Biobase: Base functions for Bioconductor Version: 2.18.0 Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon Description: Functions that are needed by many other packages...to the original thread there and I'll see that it gets answered. My guess is that you have a version of Biobase that is too new compared to the version (2.14.0) expec…

Infrastructure Cancer Biobase tkWidgets globaltest BiocInstaller BiocGenerics Cancer

updated 12.8 years ago • Shields, Rusty IMS

row.namesa vector of row names. This can be a vector giving the actual row names, or a single number giving the column of the table which contains the row names, or character string giving the name of the table column...containing the row names. If there is a header and the first row contains one fewer field than the number of columns, the first column in the input is used for the row names. Othe…

Agi4x44PreProcess Agi4x44PreProcess

updated 16.7 years ago • Massimo Pinto

0 The FDR here is Pi hat * (false/called). I'm not sure what that is supposed to mean. Which number of false am I supposed to believe? The number false as calculated by multiplying the FDR by the # called? (This makes sense...with the # false and the # called?) Excel SAM seems to circumvent this problem by multiplying the number false by Pi hat (and reporting only that product, not the number…

siggenes siggenes

updated 20.6 years ago • Jacob Michaelson

I have RNA-seq samples from yeast (~6000 genes), and there is very large variability in the total number of counts in each sample. In one of the samples I have a large number of genes with very low expression (949 genes with counts...factors for this sample, it is much smaller then what would be expected simply by taking the total number of reads. Here is a plot of the inverse of the size factors…

deseq2 rna-seq normalization

updated 9.7 years ago • gil.hornung

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20061009/ 17592f19/attachment.pl

updated 19.2 years ago • SKALKO@clinic.ub.es

20 replicates for each condition). The point is that if I rerun the BaySeq over my dataset then the number of detected genes with a specific common FDR will change. Can it be possible? For 10 times rerunning the script the number...detected genes with FDR < 0.05 are : 82, 85, 84, 87, 85, 85, 84, 86, 82, 83 > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-redhat-linux-…

baySeq baySeq

updated 13.1 years ago • Fatemehsadat Seyednasrollah

design="designmatrix",spacing=648) Error in duplicateCorrelation(object$M, design = "designmatrix", : Number of rows of design matrix does not match number of arrays I only appear to have had this problem since I changed limma...versions ??? using R 1.9.0 limma 1.6.7 Does anyone know of a easy way either contruct the above matrix OR check wether the matrix

limma limma

updated 21.6 years ago • Jason Skelton

spot copies management by LIMMA. I know that LIMMA needs all spots on the array are in the same number of copy ( e.g. each spot in double ). In my research group It is just starting a project in wich we use Agilent microarrays...positioned in a random fashion, in more than one spot for each probe. Moreover there is not the same number of copies for each probe in this block. Is LIMMA able to manag…

probe limma probe limma

updated 17.6 years ago • Erika Melissari

when i use the above Error in validObject(.Object) : invalid class "ExpressionSet" object: 1: row numbers differ for assayData members invalid class "ExpressionSet" object: 2: sample numbers differ for assayData members...signature "ExpressionSet" any help would be appreciated. thanks peevi [[alternative HTML version deleted]] </div

Annotation Annotation

updated 15.0 years ago • Peevi Ijkl

<div class="preformatted">Hi everybody, I have a question regarding comparing limma and the t-test. I compared the p values obtained from both algorithms using 100 samples in each condition. Given the large number of observations my expectation was to see high correlation between the p values. As shown below, I ran the same code in...the p values obtained from both algorithms using 100 sam…

Microarray limma Microarray limma

updated 11.6 years ago • Giovanni Bucci

gt; Thanks in advance, > > Davide Hi Davide, when looking at the actual images, are the high number of "bad" spots indicating artifacts on the slides (dirt, scratches, high and uneven background...) or just a reflection of...a large % of spots in your arrays that won't light up with your samples, it may be a good idea to identify them and remove them from the analysis... If you en…

limma impute limma impute

updated 18.3 years ago • J.delasHeras@ed.ac.uk

div class="preformatted">Hello Gentlepeople, I have been using the edgeR package to identify differentially abundant tags in an RNA-seq experiment. I was happy when the edgeR package version 2.4.6 called 41...abundant tags. However, now I am unhappy because the same analysis with edgeR package version 3.0.2 does not call any differentially abundant tags. I've compared the output of the two…

edgeR edgeR

updated 13.0 years ago • Lionel Lee Brooks 3rd

div class="preformatted">Hello, I'd like to report a missing mysql=TRUE in the useMart method for version 1.6.3 of biomaRt. I am attempting to connect to a local MYSQL database using MySQL not the webservice. I get the following...user = user, password = password, mysql=TRUE ) > packageDescription("biomaRt") Package: biomaRt Version: 1.6.3 Date: 2006-07-17 Title: Interface to BioMar…

Microarray Annotation GO annotate affy biomaRt genomes Microarray Annotation GO annotate

updated 19.2 years ago • mkeehan@lic.co.nz

<div class="preformatted">Hello, I am attempting to use the "hgug4100a" library (built using AnnBuilder) to integrate location information into a limma object. The problem I am having is how to change the annotation objects into a dataframe (once there I can use the merge function). Ideally I would have a dataframe with the following columns: Identifier Chromosome Location Any…

Annotation limma Annotation limma

updated 19.0 years ago • Daniel Brewer

library("org.Mm.eg.db") b<- addGeneIDs(annotatedPeak,"org.Mm.eg.db",c("symbol")) Error: No entrez identifier can be mapped by input data based on the feature_id_type. Please consider to use correct feature_id_type, orgAnn...or annotatedPeak Thanks, Paolo > traceback() 2: stop("No entrez identifier can be mapped by input data based on the feature_id_type.\nPlease consider to use c…

miRNA GO BSgenome BSgenome ChIPpeakAnno miRNA GO BSgenome BSgenome ChIPpeakAnno

updated 13.4 years ago • Paolo Kunderfranco

Hello everyone, I am trying to install DESeq2 package in r version 4.0.2 but it doesn't work. I have searched a lot on different pages but I couldn't find a solution. Could anyone help me

DESeq2

updated 5.3 years ago • armin.shahpari

and talented postdoctoral researcher. The postdoc will develop and apply network-based methods to identify cancer driver events from genomic and epigenomic data. Cancer is driven by alterations on all molecular levels...the puzzle of how the numerous quantitative changes (eg epigenetic or transcriptional) and copy number alterations of larger genomic regions are related to cancer initiation an…

cancer networks genomics epigenomics Job

updated 6.0 years ago • marschaefer

<div class="preformatted">Hi Bill -- On 12/31/2012 11:20 AM, wlangdon [guest] wrote: > > Today I wrote to Rafael Irizarry about this and he suggested I post my message here. > > Some time back I wrote some R code to normalise from > one to several tens of thousand Affymetrix cel files on a > (Linux) PC. > > The advantage is that it do…

Cancer Homo sapiens affy Cancer Homo sapiens affy

updated 13.0 years ago • Martin Morgan

extend = extend, shift = shift, uniq = uniq) Reading bam alignment S2.fastq.gz.bam Total number of imported short reads: 34296732 Extending reads... Creating GRange Object... Keep at most one 1 read mapping to the same...genomic location. Number of remaining reads: 19765414 Loading chromosome lengths for BSgenome... Calculating CpG density for given regions...Avvertimento: number of item…

MEDIPS CpG

updated 2.3 years ago • greta

rates (82695,51554,34786,24150). However, When I tried running the code today (updated DiffBind to version 2.8.0), I am getting the following numbers. The first two numbers are the same from dba.overlap function. __> olaprate...nbsp;817  653  484  384  202  129__ So even in the vignette the first two numbers are repeating (it should have been …

DiffBind dba.overlap

updated 7.4 years ago • romicakerketta

<div class="preformatted">I've been trying to generate a set of high-confidence peaks that are common to my ChIP-seq replicates using ChipPeakAnno. The issue I'm having is matching the number of overlaping peaks seen on the venn digram resulting from: makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1","TF2"), totalTest=(Npeaks1 + Npeaks2), useFeature=FALSE, minoverla…

Genetics ChIPpeakAnno Genetics ChIPpeakAnno

updated 13.2 years ago • António Miguel de Jesus Domingues

for the next BioC release. The package now has a 50 page user guide with several case studies. A number of statistical issues have been solved, and even very large data sets are now handled in a few minutes. edgeR users might...like to try out to new version. Best wishes Gordon </div

edgeR edgeR

updated 16.2 years ago • Gordon Smyth

you) is to generate a text files containing > a list of Homo-Sapiens validated miRNAs (microRNA-identifier, sequence) > and relative 3'UTR regions (gene-identifier, 3'UTR-sequence). Hi, Maura. See here: http://microrna.sanger.ac.uk...gt; 2) Function "hsSeqs" from package "microRNA" produces a matrix 709015x 6 > contaiing miRNA identifiers > and apparently some dat…

miRNA Homo sapiens biomaRt miRNA Homo sapiens biomaRt

updated 16.5 years ago • mauede@alice.it

Hi, I'm working on a SNP analysis project where the goal is to identify common/different polymorphisms between groups of samples. The VCF files I am using contains multiple samples...Hi, I'm working on a SNP analysis project where the goal is to identify common/different polymorphisms between groups of samples. The VCF files I am using contains multiple samples with...different genotypes at 3 pos…

VCF VariantAnnotation

updated 19 months ago • Marco

<div class="preformatted">dear list, and particularly maintainers of the graph package, i have encounter a problem with the graph package which i'll reproduce using the example code from the help page of the graphBAM() constructor function: example(graphBAM) ## run the entire example code, this creates a data.frame called 'df' df from to weight 1 a b 2.3 2 a c 2.3 3 b c 4.3 4 c d 1.0 5 d …

graph graph

updated 12.9 years ago • Robert Castelo

<div class="preformatted">Dear Bioconductor list. I have 3 time points (conditions) and 4 replicates. This is what my colDataTable looks like: condition ind B10 1_Uninfected Ind_1 B11 1_Uninfected Ind_1 B12 1_Uninfected Ind_1 B20 1_Uninfected Ind_2 B30 1_Uninfected Ind_3 B40 1_Uninfected Ind_4 B21 2_Peak_infection Ind_2 B31 2_P…

DESeq DESeq

updated 12.6 years ago • Elin Videvall

Hi, I'm working with DESeq2 DE results of microRNA expression (which I have not myself performed). I want to identify both differentially expressed miRNA and significantly stably expresssed miRNA. The DE miRNAs are obviously the...working with DESeq2 DE results of microRNA expression (which I have not myself performed). I want to identify both differentially expressed miRNA and significantly sta…

deseq2 microrna differential expression stable expression

updated 10.2 years ago • mariakarand

cancerKGML,expandGenes=TRUE); I get: Error: XML content does not seem to be XML, nor to identify a file name '' Any ideas? Many thanks, Eric -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: x86_64-unknown

KEGGgraph KEGGgraph

updated 12.9 years ago • Guest User

<div class="preformatted">Hi All, This would be extremely easy in Access, but should be manageable in R too :-) I have two tables, which are the annotation files for two platforms. I have one common identifier, the âprobenamesâ, which is used in both tables. I would like combine table 1 and table 2 into table 3. The âmatchâ is...in R too :-) I have two tables, which are the annot…

Annotation Annotation

updated 17.5 years ago • Dr Gyorffy Balazs

div class="preformatted">Hi, We are routinely using the DESeq package to identify miRNA differentially expressed in small RNA sequencing datasets from 2 biological conditions (A and B). Recently...61 36 27 Lab Web site: http://drosophile.org Post-Doc Position Available [[alternative HTML version deleted]] </div

Sequencing miRNA Genetics DESeq Sequencing miRNA Genetics DESeq

updated 14.7 years ago • Christophe Antoniewski

2] by GEO, and most importantly, it makes the analysis reproducible, and allows [tximeta][3] to identify the reference transcripts. Salmon outputs plain text quantification files called `quant.sf` but these individual...important information: which transcripts were used for quantification, the parameter settings, the version of Salmon, and even the estimated bias parameters. It would be awkward t…

salmon tximeta Tutorial

updated 5.7 years ago • Michael Love

div class="preformatted"> Dear list members, We have identified 300 genes response to a treatment in our model by cDNA microarray. We have annotated most of these sequences and...on the go. http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/ [[alternative HTML version deleted]] </div

Microarray GO Microarray GO

updated 17.2 years ago • ziping zhang

div class="preformatted">Dear all, I am working with the package GO.db (version 2.3.5) to retrieve information from GO terms and I find a large number of my GO IDs that apparently are not in the database...process". And there are many more in this situation. I is this a problem of GO database versions?. How could I find within R these l"lost" terms? Thank you in advance Ana -- Ana Conesa …

GO GO

updated 15.7 years ago • Ana Conesa

genes from the rowInd, thinking I could change this post-plot in a way, but this relates only to the number of genes found in there, so... not working! If anyone has an idea about how to solve this problem, I would be very grateful...and painful. Thanks a lot and best wishes Celine NB: I know I didn't yet upgrade to the latest version of R and BioC, and I will, but in the meantime I would app…

Annotation GO annotate affy Annotation GO annotate affy

updated 17.5 years ago • Celine Carret

Just to make sure that the problem was in affycomp in not in my method, I used the affy package version of RMA to do create the CSV file. Here's what I did: > spike133 <- ReadAffy() > spike133 AffyBatch object size of arrays...712x712 features (166358 kb) cdf=HG-U133A_tag (22300 affyids) number of samples=42 number of genes=22300 annotation=hgu133atag > bgcrma &l…

affycomp affycomp

updated 20.0 years ago • McGee, Monnie

start_position"), : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing...which can't be the problem this time, unless the example itself is incorrect) to "install the newest version of biomaRt" (which shouldn't be the problem this time because I just …

biomaRt

updated 9.2 years ago • cring

<div class="preformatted">Hello, I'm new to the Bioconductor list, and fairly new to Bioconductor itself, so excuse me if the following is a stupid question- I've been looking around the list and documentation for a while without finding my answer. The short version of my question is "What is the most appropriate way to determine if microarray-derived gene expression is associated with an…

Microarray limma Microarray limma

updated 16.7 years ago • Jon Manning

<div class="preformatted">Dear All, I experience the following problem when trying to extract reads from bam files using Rsamtools on 1000 genomes hapmap BAM file. Would be grateful for your help, thanks. Sergey ######## w=GRanges(seqnames = "1",ranges = IRanges(1000,width=400)) p2 <- ScanBamParam(which=w) res2 <- scanBam("NA12878.SLX.maq.SRP000031.2009_08.bam",p2) Erro…

Cancer HapMap Rsamtools genomes Cancer HapMap Rsamtools genomes

updated 15.5 years ago • Sergii Ivakhno

div class="preformatted"> Hi All, I have a question about analyzing aCGH data with huge number of probes on a single chromosome. We have a set of customized NimbleGen aCGH human sample data. Each sample has 40 million

aCGH aCGH aCGH aCGH

updated 17.7 years ago • pingzhao Hu

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updated 18.3 years ago • catherine xu

It shows the updated package passed BUILD and CHECK but there is an error message "built version is LOWER than in internal repository!!!" (the message can be found by moving <span style="background-color:rgb(249, 249, 248

dnashaper

updated 8.4 years ago • tsupeich

with tiff images of e.g., gels? I am getting some data from this system which translates darkness to numbers. Investigators then use the numbers as density estimates. There is a windows-based tool from Scion with similar functionality...181 Longwood Ave Boston MA 02115 USA stvjc@channing.harvard.edu -----BEGIN PGP PUBLIC KEY BLOCK----- Version: PGP 6.5.8 mQCNAzqIeGUAAAEEAMJXU941vIornTS52rl6z…

updated 23.6 years ago • Vincent J. Carey, Jr.

Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London...NW1 2BE. [[alternative HTML version deleted]] </div

IRanges IRanges

updated 11.8 years ago • Stefano Iantorno

chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as...fit, contrast.matrix) fit2 <- eBayes(fit2) #### top list topTable(fit2, coef=1, adjust="BH", number=20, sort.by="M") library(hgu133plus2.db) u<-mget(row.names(fit2),…

Clustering affy limma Clustering affy limma

updated 15.8 years ago • Maxim

<div class="preformatted"> Dear list, I have been trying to apply the MGSA method for gene set analysis to my data by using the mgsa package that is part of the Bioconductor release, but so far I haven't been able to make it work. When using the package's readGAF function to create the list of gene sets from the GO categories with the Rat files downloaded from the GO webpage (http://www.g…

GO rat2302 Category mgsa GO rat2302 Category mgsa

updated 13.0 years ago • Guest User

install Bioconductor 2.4 1. Install R 2.9.0. Bioconductor 2.4 has been designed expressly for this version of R. 2. Follow the instructions here: http://bioconductor.org/docs/install Please visit http://bioconductor.org for...descriptions. AffyTiling Easy extraction of individual probes in Affymetrix tiling arrays betr Identify differentially expressed genes in microarray time-course dat…

Microarray qPCR Metabolomics Annotation Normalization graph flowCore Microarray qPCR

updated 16.7 years ago • Patrick Aboyoun

Hi there, I got the following error message when trying to load the mzR package. Please help. Thank you in advance. Input: ```r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("mzR") library(mzR) ``` Output: ```r Loading required package: Rcpp Warning message: In fun(libname, pkgname) : mzR has been built again…

mzR

updated 4.8 years ago • Sarah

We however recently updated our Singularity image, and we now work with a newer DiffBind package version. Unfortunately, the new(er) versions either introduce a new bug (see below) or at least an undocumented and hard to understand...just fine when running with DIffBind 2.14, but results in 0 consensus peaks with a newer DiffBind version. Can someone help? I can provide the rds file of the dba o…

DiffBind

updated 3.6 years ago • chrarnold

six. There's a total of 18 sample groups (T4.LL.FW, T4.LL.SW, T4.SP.FW, T4.SP.SW, etc.) I want to identify genes that are differentially expressed between the different light treatments, at each timepoint, utilizing...and overlapping DEG's, providing the opportunity to make f.ex. a Venn diagram "time-series", showing number of unique and shared DEG's between treatments at each timepoint. Howeve…

EdgeR ANOVA t-test contrast

updated 8.5 years ago • Maiv

div class="preformatted">Hello, I have a custom Affy Genechip that was designed using a draft version of a bacterial genome. We now have the finished version of the genome sequence available, so I would like to re-annotate...the microarray probes to reflect the new genome sequence and gene numbering system. This problem appears to be something that many groups deal with on a regular basis, a…

Annotation cdf affy Annotation cdf affy

updated 14.5 years ago • Ariel Grostern

DBI Now preprocessing raw data of GSE23402: Collapsing expression values to their median... Using identifier as id variables Now preprocessing raw data of GSE23402: Annotating expression values with SYMBOL... Now preprocessing...Now preprocessing raw data of GSE26428: Collapsing expression values to their median... Using identifier as id variables Now preprocessing raw data of GSE26428: Annotati…

Annotation Preprocessing hgu133plus2 hgug4112a

updated 11.3 years ago • Guest User

div class="preformatted">Hi There Jenny I've tried your steps a number of times, but keep getting the same error below! Could you kindly help? Thnx Ernest Loading required package: graph Loading...LoadLibrary failure: The specified module could not be found. [[alternative HTML version deleted]] </div

updated 16.5 years ago • Ernest Hobson