Bioconductor Forum

annotation library! > x.lumi Summary of BeadStudio output: Illumina Inc. BeadStudio version 3.3.7 Normalization = none Array Content = HumanHT-12_V3_0_R1_11283641_A.bgx.xml Error Model = none DateTime = 18...QC information: Please run summary(x, 'QC') for details! I am using R version 2.7.1 (2008-06-23). > packageDescription("lumi")…

Microarray OneChannel Annotation Normalization probe Biobase annotate genefilter affy vsn

updated 17.1 years ago • Steve Taylor

and as a student in biomathematics and attending a paper of computational biology I'm asked to identify significantly expressed genes by a SAM analysis. We are working on the raw data set provided by Wang [1] at GEO [2] and...wd") # load required libraries library(affy) # for Affymetrix chips library(siggenes) # identifying significant genes library(hgu133a2.db) # to map the a…

Prostate hgu133a2 probe affy siggenes ASSIGN Prostate hgu133a2 probe affy siggenes

updated 15.9 years ago • Torbjörn Klatt

error: Error in validObject(.Object) : invalid class “MRexperiment” object: 1: feature numbers differ between assayData and featureData invalid class “MRexperiment” object: 2: featureNames differ between assayData

MRexperiment metagenomes metagenomeSeq

updated 4.8 years ago • Laura

How many [signaling pathway][1]s are founded? [1]: https://www.bocsci.com/signaling-pathway.html

chemistry

updated 2.9 years ago • beikrystal25

Hi, I feel the chromosome information is wrong in the output of the cpg.annotate command. Could you check what's wrong here? > summary(as.factor(myannotation1$CHR)) 1 2 3 4 5 6 7 8 …

DMRcate

updated 9.5 years ago • yuping.zhang

Dear List, I have a basic statistical question regarding a Microarray data set. However, I am not an statistician. I was told the following problem can be modeled in R/ S_PLUS. I have a data set with 3 replicates for the control and 3 replicates for experimental samples for a particular experiment. I performed a t.test and adjusted the p. values for the false discovery rate. Choosing a p val…

Microarray Microarray

updated 19.7 years ago • Khan, Sohail

printed and they are 18.8mm in diameter. Between those disks are 2 rows of 5 seeds. We are trying to identify the length, width, and area of each hull and kernel. That way, we can directly identify the kernel/hull ratio for breeding...without excess. 3. Would it make sense to create a code loop that uses shapeStats' s.area and the number of rows/identified objects to adjust the fillHull paramet…

EBImage

updated 24 months ago • Brian

min.n, offset = offset, method = method.bin, : With 1273 genes and setting the parameter minimum number (min.n) of genes per bin to 500, there should technically be fewer than 2 bins. To make estimation of trended dispersions...possible we set the number of bins to be 2. 2: In binGLMDispersion(y, design, min.n = min.n, offset = offset, method = method.bin, : With 1273 genes and setting...…

RNASeq edgeR RNASeq edgeR

updated 12.5 years ago • Eduardo Andrés León

C, + test.type = "ttest", test.method=c(1,1,1,1), n.perm=10) It gives this error: Error: The number 1 test is not estimable > traceback() 3: stop(paste("The number", i, "test is not estimable"), call. = FALSE) 2: checkContrast(model...three age classes. Thanks a lot in advance for any input. Cheers, Vicencio > sessionInfo() R version 2.11.1 (2010-05-31) i386-pc-mingw32 locale: […

maanova maanova

updated 13.6 years ago • V. Oostra

<div class="preformatted">Hi Michael, > The error is new because you are now using the v1.2 of DESeq2 which came > with the Bioconductor 2.13 release this month. Maybe the system you are > working on automatically upgraded? > > The error you see is saying that you cannot subset the results DataFrame > with a vector that contains NAs. In the newest…

DESeq2 DESeq2

updated 11.5 years ago • Marko Laakso

Thank you very much in advance. Here is `` R CMD BiocCheck `` This is BiocCheck version 1.17.23. BiocCheck is a work in progress. Output and severity of issues may change. Installing package... * Checking for...version number mismatch... * Checking vignette directory... This is a software package # of chunks: 45, # of eval=FALSE: 9 (20%) * Checking vers…

package development

updated 7.2 years ago • ntueeb05howard

fullXmlQuery, : > 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 on the support...annotation, but with ensembl37 is also fine. I appreciate your help! Thanks, A PS. ```r > R version 4.0.2 (2020-06-22) > package.version("bi…

GO biomaRt

updated 4.3 years ago • A

errno: 13) Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", "chromosome_name", : Number of columns in the query result doesn't equal number of attributes in query. This is probably an internal error, please...report. > sessionInfo() R version 2.9.0 (2009-04-17) i486-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US

Cancer biomaRt Cancer biomaRt

updated 16.4 years ago • Aedin Culhane

the offspring, mother and father vectors be scan ids or scan/subject names? My scan names are not numbers and so these vectors would not satisfy the requirement in the manual of "a vector of offspring/father/mother ID numbers...id of the offspring? Any advice would be greatly appreciated. Thanks, Sam > sessionInfo() R version 2.15.1 Patched (2012-07-01 r59713) Platform: x86_64-unknow…

GWASTools GWASTools

updated 13.2 years ago • Samuel Younkin

<div class="preformatted">Hi everybody, I have a question regarding comparing results from a t-test and limma. 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 us…

Microarray limma Microarray limma

updated 11.6 years ago • Guest User

gt; sessionInfo()) R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets...gt; data AffyBatch object size of arrays=602x602 features (50972 kb) cdf=RAE230A (15923 affyids) number of samples=18 number of genes=15923 annotation=rae230a > res <- justPlier(data, get.affinities = TRUE) …

cdf probe Biobase affy plier cdf probe Biobase affy plier

updated 20.2 years ago • Jeremy Gollub

files: ".tsr" and ".pep". I only want to import the ".tsr" files as these are the processed trimmed versions of the ".prp" files. When I simply open the files using my native text editor they are not fast format which I have worked...EDLAANNPAI QNIRLRHENK DLKARLENAM EVAGRDFKRA ___ I would like them to be import with the identifier as  "emm1.0"  (either from first line…

r biostrings decipher

updated 7.9 years ago • reubenmcgregor88

na.rm = TRUE) a.med <- a.med/(prod(a.med))^(1/narrays) multiplying 400 relatively small numbers can easily reach R's limit as far as doubles are concerned. > 6^400 [1] Inf Wouldn't it be better to be working in log space...instead? Francois > sessionInfo() R version 2.1.0, 2005-04-18, x86_64-unknown-linux-gnu attached base packages: [1] "methods" "stats" "grap…

updated 20.2 years ago • Francois Pepin

div class="preformatted"> in the simple annotation objects chr entries should be the original chr numbers or indices into chrMap? in your withShortRead example THRO55C.1 had VIII translated to 8 in the simple annotation...when in chrMap it has location 13 in chrMap. thank you Nitzan -- output of sessionInfo(): R version 2.11.0 (2010-04-22) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=e…

Annotation Annotation

updated 14.1 years ago • Guest User

No package 'file29282' was found > in: packageDescription(p, lib = lib, fields = pkgFlds) > 2: number of columns of result > not a multiple of vector length (arg 2) in: rbind(retval, c(p, > lib, desc)) > Error: package 'reposTools...were the > tricks? > Thanks, > Anton [[alternative HTML version dele…

updated 20.6 years ago • Belooussov, Anton

Dear all, I have a large RNA-seq data set with 63 samples in 12 condition with different number of replicates. I want to run R on the server to make it faster, but I have this error. Would you please help me. error: "Error...1\]\] : subscript out of bounds Calls: DEXSeqDataSetFromHTSeq Execution halted" I have R version 3.2.0. here is a short example of the codes I am using: re…

DEXSeq

updated 10.4 years ago • rahel14350

div class="preformatted">Hi, I have a large number of CEL files (~4000) that I would like to rma normalise. Just reading in the files and rma normalising them is not possible...Could someone please help me get around this? Thanks, Emma [[alternative HTML version deleted]] </div

BufferedMatrix BufferedMatrix

updated 12.9 years ago • Emma Reick

specified=""> data AffyBatch object size of arrays=1164x1164 features (9 kb) cdf=2.0 (??? affyids) number of samples=15 Errore in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment...Bologna, Italy ----------------------------------------------------- [[alternative HTML version deleted]] </rma(data)></div

hgu133plus2 cdf hgu133plus2 cdf

updated 16.4 years ago • Alberto Goldoni

the maploc argument is "the locations of marker on the genome. Vector of length same as the number of rows of genomdat. This has to be numeric." So it has to be numeric from the DNAcopy documentation. Is it the first value...of the two 175484345, or something else that I am missing completely? I [[alternative HTML version deleted]] </div

DNAcopy DNAcopy

updated 11.4 years ago • Nikolas Balanis

Data AffyBatch object size of arrays=1190x990 features (25 kb) cdf=HuGene-1_1-st-v1 (??? affyids) number of samples=20 Error in (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE, : hugene11stv1cdf is not a valid...May someone let me know how I could fix this problem? Thanks, Jerry [[alternative HTML version deleted]] </div

Microarray cdf affy PROcess oligo xps Microarray cdf affy PROcess oligo xps

updated 12.1 years ago • Jerry Cholo

We're doing 10 complete permutations Error in d.perm[, i] <- sort(tmp$t.num/(tmp$t.denum + s0)) : number of items to replace is not a multiple of replacement length In addition: Warning message: There are 127 variables with...variance. These variables are removed, and their d-values are set to NA. [[alternative HTML version deleted]] </div

updated 17.4 years ago • D F

div class="preformatted">Is there anyway to covert a lumi NuID ("xl5dFtdFTQCRSSkbwc") to a UCSC identifier ("uc002qsd.4") taken from Genomic Features? Chris </div

lumi lumi

updated 13.0 years ago • Fenton Christopher Graham

Oggetto: Re: [BioC] BioMart error occurred again I think that you have asked this question (a number of times) before. Please see Steffen's answer to you via the link (and please note Sean's requests): http://thread.gmane.org...25 759/focus=25778 Within a 7 hour period, there could be a number of things that can occur between your connection to Biomart. Batch queries would be the way forward a…

biomaRt biomaRt

updated 16.1 years ago • mauede@alice.it

phase of the analysis, I realized that the data was previously generated using a Galaxy-based version of DESeq2 v 1.34.0 and I used version 1.40.1 in RStudio (see below). ![Volcano Plots generated using Galaxy and R(RStudio...I am including (see below) as an example, information about gene A. I am also including the raw numbers for the gene, the normalized counts coming from the dds object (RStu…

DESeq2

updated 2.5 years ago • peTTU

div class="preformatted">Hi there, I found the number of pathways in KEGGPATHID2NAME is 390 while that in KEGGPATHID2EXTID is 3152. Am I missing something? BTW, the pathway...xx[1:3] } } > length(xx) [1] 3152 > sessionInfo() R version 2.14.1 (2011-12-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Chinese (Simplified)_Peopl…

Pathways cycle Pathways cycle

updated 13.4 years ago • Ed

the genes of two different pathways are correlated or anti-correlated or no correlation at all. The number of genes in the two pathways are different, that's why a simple scatter plot will not be effective. Is there a simple way...Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]] _______________________________________________ Bio…

Microarray Pathways GSEABase Microarray Pathways GSEABase

updated 13.0 years ago • Robert Castelo

I'm analysing RNA-seq data from two datasets (from healthy samples) and created a unique GTF file to identify new isoforms by using StringTie. Then I used Salmon to estimate their TPMs, but I have some questions hoping anyone...interested in DGE nor DTU as I don't have any "condition" to compare against with as my goal is to identify novel isoforms of my gene of interest. Is there also any other …

tpm RNASeq tximport

updated 4.3 years ago • karlaarz

with their data. Perhaps this can be done in R itself...? or, is there a web API I could use to identify packages that are using rhdf5 and (in a perfect world) identify the important people behind those packages.  My

rhdf5 hdf5 dependencies

updated 9.4 years ago • thabermann

Hi, <span style="line-height:1.6">I have used bump hunter function for two populations (control and disease represented by status column) using the following formula</span> <code><span style="line-height:1.6">designMatrix <- model.matrix(~ status)</span></code> <span style="line-height:1.6">For each of control and disease populations,within each…

bumphunter

updated 9.3 years ago • Asma rabe

tableNames data = dbReadTable(dbconn,"MouseWG6_V1") head(data) The column ProbeId contains identifier "105290026" which is in the flat file on http://www.switchtoi.com/pdf/Annotation%20Files/Mouse/MouseWG- 6_V1_1_R4_11234304_A.zip...under the column Array_Address_Id and has a proper identifier of "ILMN_1229450". Hope this helps and that it might be corrected sometime in the future, Nenad Nena…

Annotation probe biomaRt Annotation probe biomaRt

updated 16.8 years ago • Nenad Bartonicek

files using both marray andlimma functions The first things to try are 1. Upgrade to the latest version of limma from http://bioinf.wehi.edu.au/limma 2. Check with your associate that the genepix gpr files really have...that you really need files as they are straight out of GenePix. You should also tell us what versions of R and the packages you are using, type: version packageDescription("lim…

limma marray limma marray

updated 21.3 years ago • michael watson IAH-C

to rephrase my question: Beyond visualization, I wanted to know if it is possible for DiffBind to identify differential peaks across all 4 different conditions. Currently, when we set a `` dba.contrast() ``, it only compares between...4 different conditions (representing different "subtypes" of a disease condition) and would like to identify differential peaks among all 4 different conditions (id…

diffbind chipseq

updated 7.6 years ago • Shamaine

of vectors consist of 0 and 1. But in the new version (1.6.2) I found that the vectors get from peak sets contains also a number (rather than 0 and 1). I might lost when reading...You can set bParallel=FALSE to do this -- it is a lot slower though! You can also try to lower the number of cores being used when it runs in parallel, e.g. > DBA$config$cores = 2 2. To get the numbers of peaks…

Transcription Cancer DiffBind MMDiff Transcription Cancer DiffBind MMDiff

updated 12.3 years ago • Rory Stark

where 12 is the minimum group size y <- y[keep,] dim(y) The above filtering reduces the number of tags from 90,000 to ~ 50,000. After filtering a total of 29 genes are differentially expressed (adjusted p-value <= 0.05...of how I ran edgeR? On perhaps a related note, should I alter my code because I have a fairly large number of biological replicates. Below is the entire code I a…

edgeR edgeR

updated 12.8 years ago • Mark Christie

Dear Bioconductor community, based on a current project aiming to decipher prognostic biomarkers that driving the response to chemotherapy in breast cancer, we are trying to analyze external public datasets to validate in house findings; on this premise, on an rnaseq gene expression dataset of neo-adjuvant treated patients with multiple time points: T1 is the “pre-treatment” timepoint, T2 …

edgeR RNASeq DifferentialExpression TimeCourse

updated 4.4 years ago • svlachavas

the intersect of significant genes (probably loss of power due to lower library sizes and sample number) Findings: Y results in a major increase in identified significant genes compared to X. Which way would be the best to

rnaseq deseq2 differential expression batch effect replicates

updated 6.2 years ago • Nik dAK

I am trying to use DESeq2 to identify differentially expressed genes across different rodent species as part of a larger project on rodent evolution...is.na(e2) : longer object length is not a multiple of shorter object length ``` I have tried a number of ways, and read many documents and forum posts online, but can't seem to get past this stage. So I am just trying to work

deseq2 rna-seq

updated 6.5 years ago • Emma

they have large fold-changes. Are the counts of these genes recognized as outliers? The R code to identify differentially expressed genes and plot MA-plot are here. library(pasilla) library(DESeq2) pasCts <- system.file...col = ifelse(res$pvalue < 0.1, 2, 1)) Outputs of `` sessionInfo `` are here. R version 3.4.2 (2017-09-28) Platform: x…

deseq2

updated 7.9 years ago • jQ

I have to analyse BeadChip Methylation Data. Since I don't have replicates in my experiment, I'm thinking of using the package 'DSS' for the analysis. This package takes data in count format for each CG position: chromosome number, genomic coordinate, total number of reads, and number of reads showing methylation, like: ```r chr pos N X chr18 3014904 26 2 chr18 303103…

methylationArrayAnalysis illuminaio beadarray DSS bsseqData

updated 3.8 years ago • Jojo

GSE2) }) <strong> data <- reactive({ validate( need(input$number != "", "Please enter an input here") )</strong> }) qualC <- reactive({ value=as.vector(input$checkGroup) value=sprintf('%s_%s.pdf',value...headerPanel("Representation"), # Sidebar with controls to select a dataset an…

R validate shiny

updated 10.2 years ago • alptaciroglu

<div class="preformatted">You seem to have a major problem with your analysis, which is that you don't seem to have incorporated the dye swaps into your design matrix at all. You define a vector call 'vector', but then make no use of it. Perhaps you should investigate the use of the functions in limma such as modelMatrix() which use targets frame to construct design matrices. As far as the…

limma limma

updated 20.8 years ago • Gordon Smyth

Actually on checking back through the records, I can see that none of the Bioconductor release versions of limma would have given the below error. You must be using an in-between version of limma from between Feb 8 and March...the version number of software that you're asking questions about, and that it is a good idea to try updating to current software...with gls.series in limma >Cc: bio…

limma limma

updated 21.2 years ago • Gordon Smyth

binding failed: Symbol not found: _utimensat Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.13) Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol...not found: _utimensat Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libR.dylib (which was built for Mac OS X 10.1…

install GenomeInfoDbData

updated 5.6 years ago • lina.bird

required package: siggenes Loading required package: multtest Latest major changes in siggenes: Version 1.9.27: EBAM update completed. Added new vignette. Version 1.11.7: Improved version of EBAM for categorical data. Version...1.11.9: Added findDelta for determining the number of genes called differentially expressed for a given FDR, and vice versa. Attaching package: 'siggene…

siggenes siggenes

updated 18.3 years ago • Kimpel, Mark W

packages (ChIPseeker) in R/BiocManager This is the warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install: 'ChIPseeker'. Here is the code and error I get: ``` > BiocManager...for details replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31) …

Bioconductor BioCManager ChIPseeker

updated 3.0 years ago • ASIF

on two treatments(trtR/trtNR) and the sampling is done at 7 different time-points. I have different number of replicates: for trtR two replicates and for trtNR 5 replicates for each time-points (some time number of replicate...expressed at each time point and also across all time points. Then a likelihood ratio test to identify differentially expressed genes. I learned from this question https://…

deseq2 GLM timecourse

updated 8.1 years ago • rahel14350

209 ageing-related files. I download the summary file. In the summary file, I can see the GSEXXXX number for each GDSXXXX number. 2. Using a python script and FTP, I can pull down the CEL files for each GDS file (e.g. one FTP address...Affy package. 5. Then I will do a hierarchical clustering and PCA to identify potential outliers in each data set using…

microarray meta-analysis gene expression

updated 6.9 years ago • StephK

<div class="preformatted">At 08:00 PM 16/06/2006, bioconductor-request at stat.math.ethz.ch wrote: >Date: Fri, 16 Jun 2006 11:30:18 +0200 >From: Pedro L?pez Romero <plopez at="" cnic.es=""> >Subject: [BioC] decideTests with nestedF >To: <bioconductor at="" stat.math.ethz.ch=""> >Content-Type: text/plain > >Dear list, > &…

probe limma probe limma

updated 19.5 years ago • Gordon Smyth

s24vss48",number=17328,adjust.method="no ne",p.value=1) write.table(s24vss48,file="s24vss48nofdr.txt",sep="\t") s48vss96<-topTable(fit2...coef="s48vss96",number=17328,adjust.method="no ne",p.value=1) write.table(s48vss96,file="s48vss96nofdr.txt",sep="\t") c0vsc24<-topTable(fit2...coef="c0vsc24",number=17328,adjust.method="none ",p.value=1) write.table(c0vsc24,file="c0vsc24nofdr…

genefilter multtest limma genefilter multtest limma

updated 16.8 years ago • Sally

ie mock 4h versus dex 4 h and mock 12 h vs dex 12 h. As part of our analysis we would like to identify regions of DNA that do not fall within annotated exons (ie unannotated genes). Is anyone aware of an existing R algorithm...take a more automated and objective approach using R. Finally, has anyone used the Tiling Array to identify differential expression? And if so, what approach was used? T…

updated 18.4 years ago • Pia Sappl

as a slope...clarification would be helpful here). From my previous analysis in DESeq, I've identified which genes change over time relative to control using a LRT analysis.  Now I would like to identify the pattern

deseq

updated 8.4 years ago • chimeric

is probably batch effect: let's say batch A and B. For A, I have 7 controls and 7 cases (clinical identified). For B, I have the same 7 controls and other 7 pre-cases (preclinical identified) I wanted to know if I can analyze

RNASeq

updated 10.6 years ago • Lorena Pantano

in methylation (one with 2 levels, one with 4 levels, and one continuous) I have used limma to identify DMPs using these matrices successfully (I think) I want to use the bumhunter method in minfi to look for DMRs but there...c(1,2) but this threw up an error [bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.2). [bumphunterEngine] Computing coefficients. …

limma bumphunter methylationArrayAnalysis minfi

updated 2.7 years ago • edward.esiribloom

advices to have at least 25 arrays to use the method. (I'll send you a snippet of code to run and identify more precisely where the problem comes from). > What is the name short name for R. Izarry et al. method ? I don't like avgdiff...value computation from the probe level data. Slight difference remain between them. The next version of affy will offer a better integrated system for tha…

probe affy probe affy

updated 23.6 years ago • Laurent Gautier

<div class="preformatted">I have an Affy experiment with a very high level of differential expression. It is a one-way ANOVA with 6 treatments, 2 replicates per treatment. We ran both SAM (excel version) and limma, and had very good agreement between them in terms of ranking the genes by the test statistic. For any set of...It is a one-way ANOVA with 6 treatments, 2 replicates per treatm…

affy limma convert affy limma convert

updated 21.5 years ago • Naomi Altman