Bioconductor Forum

gt; BiocManager::install("PCAtools") Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23) Installing package(s) 'PCAtools' also installing the dependencies ‘sparseMatrixStats’, ‘S4Vectors’, ‘IRanges’, ‘ScaledMatrix...running the following in an R session sessionInfo( ) ``` > sessionInfo() R version 4.2.1 (2022-06-23) Platform: aarch64-apple-darwin20 (64-bit) …

PCAtools bioconductor

updated 3.5 years ago • pterry

30 B-2340-Beerse, Belgium Below you`ll find the logfile/environment settings for both test runs. ****************************************************************** Log for expressionSetRma<- rmaPara(files) => OK ****************************************************************** ubuntu at ip-10-239-95-215:~/test$ cat runAffyPara.R.log.withoutcdf R version...Type 'contributors()' …

Microarray affyPara Microarray affyPara

updated 13.6 years ago • Wetzels, Yves [JRDBE Extern]

rma-gene-full.chp") ``` There is no output since it just keeps crashing. The data I used is public and can be downloaded at this website:https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2252974. Go to the bottom

affxparser r Bioconductor

updated 3.6 years ago • Cameron

I have a public scRNA dataset of an expression matrix normalized by the deconvolution method in scran (just a txt file of counts). The

DifferentialExpression scRNAseq scran

updated 4.9 years ago • LUCIA

or not. Btw. the vignettes of it seem to a bit outdated, e.g. the 'writeAnnData2Pkg' function is not public any more. So my questions are: 1) Is AnnBuilder the right tool for this? 2) If not, are there any "right" tools? I don't mind creating

miRNA Annotation AnnBuilder miRNA Annotation AnnBuilder

updated 17.0 years ago • Gábor Csárdi

of Biostatistics, Section on Statistical Genetics University of Alabama at Birmingham 327 Ryals Public Health Building 1665 University BLVD Birmingham, AL 35294 Tel: 205-996-4154 Fax: 205-975-2540 Email: xcui@uab.edu [[alternative

Sequencing Sequencing

updated 14.5 years ago • Xiangqin Cui

Lang Chen Research Assistant Department of Biostatistics Section on Statistical Genetics Ryals Public Health Building, Suite 343A University of Alabama at Birmingham 1530 3rd Ave S Birmingham, Alabama 35294 Tel 205-9757772

DOSE DOSE

updated 22.7 years ago • Lang Chen

preformatted">Hi, I would like to check for differential expression on arrays downloaded from public databases. I was reading somewhere that it might be not very wise to normalize together arrays produced from different

updated 18.8 years ago • marco zucchelli

Hi, I'm gonna simulate some RNA-seq read counts data from a real data set for publication purposes. My problem is I can't download big Fasta files. So I want to obtain the count matrix using galaxy and then

simulation count matrix RNA-seq Polyester

updated 8.1 years ago • fa.gholizadeh89

for the plot. I'm wondering whether there is function to fine-tune the visualization of plot for publication purpose. Another question regarding to the results. "fisherGOProfiles" is the function to find the significant

GO GO

updated 12.0 years ago • Bai, Bing

description of the algorithm that matchPWM implementation is based on, preferably a peer-reviewed publication. I apologize in advance for not being able to see the obvious answer here. But the reference (Wasserman and Sandelin

biostrings matchPWM

updated 11.4 years ago • Yue Li

array 16 >Corrected array 17 >Corrected array 18 >Warning messages: >1: Produced NaNs in: log(x) >2: Produced NaNs in: log(x) >3: Produced NaNs in: log(x) > >I find that some NaNs occur when running the code "out <- normexp.fit

Microarray limma Microarray limma

updated 18.9 years ago • Gordon Smyth

<div class="preformatted">We have a project with a somewhat spectacular design: two cell types in trans-well culture, each cell population from a human donor. In each experimental setup, we use one set of donors, treated with ~10 different perturbagens performed as a single replicate, plus a vehicle control performed in duplicate; we repeat this setup independently 5 times with 5 different…

PROcess edgeR DESeq PROcess edgeR DESeq

updated 12.8 years ago • Aaron Mackey

Enter the body of text here Recently, I use the DESeq2 to analyze a data, but there is a question is that the DESeq2 tutorials point the quickly start ，which use the code ``` ``` dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design= ~ batch + condition) dds <- DESeq(dds) resultsNames(dds) # lists…

DESeq2 Normalization

updated 4.6 years ago • Golden-proteogenomics

and normalized matrix of probes (no summary!). However, the values of that matrix do not seem to be log transformed. My question is whether I'm doing something wrong here. this is the protocol: cel.all <- ReadAffy(filenames

updated 21.7 years ago • Arne.Muller@aventis.com

used as a reference, Green or Red, when the maNorm() function generates the "maM" matrix. Does M is log(R/G) or vise versa. I'm asking that because I analyze a dye swap experiment and I realize that I have to swap my self the reference

Normalization Normalization

updated 22.6 years ago • Ron Ophir

Hi All, I was wondering if anyone had any idea how one might put error bars on the log fold changes calculated by edgeR? I'd like to do this so I can show examples of differentially expressed genes on a bar plot

qPCR qPCR

updated 13.0 years ago • Ian Sudbery

all the normalisations provided by the package and it appears that the median normalisation with log-transformed data and a multiplicative model show the best performance. So finally I have negative and positive values

cellhts2

updated 10.4 years ago • User34591

data sets are one channel (with normalised intensity) and one is two channel (common reference) with log 2 ratio of the two channels. Can I just log2-transform the normalised intensity in the one channel data sets and compare

RankProd RankProd

updated 13.9 years ago • Barbara Bo-Ju Shih

KEGG database. and I have got list of genes and pathways that are represented by the dataset. it has log fold change data as well. But I am not able to figure out which data I should provide to the pathview? can someone please tell

rnaseq pathview data visualization

updated 10.2 years ago • amoltej

nbsp;I am getting: <pre> > maQualityPlots(data) [1] FALSE Error in plot.window(xlim, ylim, log, asp, ...) : need finite 'ylim' values In addition: Warning messages: 1: no non-missing arguments to min; returning Inf 2: no non-missing

arrayQuality

updated 10.8 years ago • Bandyopadhyay, Somnath Som

either "scaledTPM" or "lengthScaledTPM". The limmaUsersGuide() suggests doing `` logCPM <- cpm(y, log = TRUE, prior.count = 3) ``. I thought that since cpm() is an edgeR function it would use the y$offset, but looking at the code of cpm.DGEList

tximport limma limma-trend edgeR

updated 8.3 years ago • Jenny Drnevich

I created a flowFPModel from a flowSet using two logtransformed parameters. One of these parameters (FL3) was used for a rectangleGate to filter out background noise, thus, the original range of -1 to 3 was narrowed down to 0 to 3. When I make a plot of the resulting model or have a look at the bin boundaries, it shows that the model still spans the original range of -1 to 3. I do not know if thi…

flowCore flowFP flowFPModel

updated 5.9 years ago • palffy.karoly

lt;= 0.001),0.001) Beta <- replace(Beta,which(Beta >= 0.999),0.999) Y <- log((Beta/(1-Beta)),2) Bumps <- bumphunter(Y, design=X, chr=Anno[bumphunter.idx,]$chr, ...... Does the DMR not still support the multi-phenotypes

ChAMP DMR

updated 5.6 years ago • olive8306

each.="" experimental="" fifth="" for="" four="" give="" had="" has="" hope="" i="" is="" know="" li="" log-transformed="" lot="" many="" me="" meaning.="" no="" of="" or="" p-value:="" parameters:="" ppde="" ppde(<p)="" raw="" remove="" replicate="" replicates="" results="" set="" size

updated 13.8 years ago • Li Zhang

pasted, I will guess it is Linux. When you start R, what does capabilities() say? The installation log for WidgetTools is fairly clear in telling you that there is a problem with using R's tcltk package. So you will want to investigate

Cancer widgetTools Cancer widgetTools

updated 18.7 years ago • Seth Falcon

A post-doctoral position in bioinformatics and computational biology is available in Prof. Julie Zhu's group in the Department of Molecular, Cell and Cancer Biology at the University of Massachusetts Medical School, located in Worcester MA. Research projects in Dr. Zhu's group include (1) development of bioinformatics algorithms and tools for integrative and interactive analysis of multi-omics…

single cell sequencing multi-omics data mining and integration Job

updated 6.4 years ago • Julie Zhu

grep("BAC1|BAC2|BAC3", RG$genes$Name) RG.final<-RG[peptides, ] RNorm<-normalizeBetweenArrays(log(RG.final$R,2)/log(RG.final$Rb,2), method="quantile") GNorm<-normalizeBetweenArrays(log(RG.final$G,2)/log(RG.final$Gb,2), method

limma limma

updated 15.7 years ago • K.Z.Nambiar@bsms.ac.uk

Dear BioC list, I'm analyzing for the first time old data from Agilent two colors arrays (array version G4110B). As experimental design, I have 3 time points x 2 replicates at each time point in a treated vs control experiment. Arrays were hybridized at 2 different times, so I decided to reduce an evident batch effect using also the "NormalizeBetweenArrays" function after "NormalizeWithinArrays"…

marray agilent twochannel normalization limma

updated 11.0 years ago • Andrea Grilli

a data file (several rows shown here): -- start data file -- Mean M/Z SD M/Z N Mean Int (Log) SD Int (Log) 59.99434 0.004952 100 7.5543 0.3918 67.95295 0.006149 100 4.4477 0.5896 68.95164 0.006361 100 7.1036 0.5675...0.00673 0.00677 ... $ N : num 100 100 100 100 99 100 100 100 99 95 ... $ Mean.Int..Log.: num 7.55…

ASSIGN ASSIGN

updated 18.4 years ago • Nathan Haigh

When I use Biostring pairwiseAlignment, I can't get the same result with EMBOSS needle using the same parameters. ```r library(readr) library(dplyr) library(Biostrings) EDNAFULL<-read_tsv("/run/media/panxiaoguang/myLinux/Zebrafish/EDNAFULL",col_names = T)%>% tibble::column_to_rownames(var="index")%>% as.matrix() EDNAFULL A T G C S W R Y K M B…

Alignment Biostrings

updated 3.1 years ago • 潘晓光

CRAN: https://cran.rstudio.com/ Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31) Installing package(s) 'glmGamPoi' trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/macosx/big-sur-arm64

glmGamPoi

updated 3.2 years ago • sina.tadayon

Mysession info is as follows and the error message is above. > sessionInfo() R version 4.2.1 (2022-06-23 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 Matrix products

SEC_E_ILLEGAL_MESSAGE(0x80090326) handshakefailed

updated 3.3 years ago • moiz_aftab

Chinese softshell turtle genes (PelSin_1.0) PelSin_1.0 sessionInfo( ) R version 4.1.3 (2022-03-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS Matrix products: default BLAS: /usr/lib/x86_64

biomaRt

updated 3.8 years ago • Charlotte

FALSE it still gives and error: My sessionInfo (only some of it below): R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 10 (buster) **_Attempt 1:_** ```r # Converting DMR list results.ranges

DMRcate R DMRcatedata Markdown

updated 2.9 years ago • yr542

DESCRIPTION', probable reason 'No such file or directory' # > sessionInfo() R version 4.1.3 (2022-03-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044) Matrix products: default locale

phyloseq

updated 3.6 years ago • Ezra

Hi, I'd like to revisit some earlier posts regarding running `DEXSeq` on a large number of samples, similar to past posts [like this one](https://support.bioconductor.org/p/130486/). My eventual goal is to run `DEXSeq` on a subset of TCGA tumors; my full dataset comprises ~300 samples x ~700k junctions, and I (perhaps expectedly) have run into issues where `estimateDispersions(dxd)` will run for…

DESeq2 glmGamPoi DEXSeq

updated 3.2 years ago • jeremymsimon

mouse package?** That's what I get if I look them up on Entrez, but can't retrieve the codes, nor I have any idea how to turn this list into an importable file... ![enter image description here][1] The Entrez IDs aren't included

annotation entrez gene ids software error

updated 6.8 years ago • Raito92

what a BI_SNP array is and what cdf file I have to use for it? At first glance neither Nettaffx nor the Bioconductor annotation packages seemed to give me an obvious solution. Thanks, Claus ********************************************************************** **** Dr Claus-D. Mayer | http://www.bioss.ac.uk

SNP Annotation cdf affy PROcess oligo SNP Annotation cdf affy PROcess oligo

updated 16.7 years ago • Mayer, Claus-Dieter

div class="preformatted">Dear edgeR users, I am not a statistician nor R programming geek, please forgive me if I ask stupid question. I have RNA-seq data for 2 different genotype of trees with

edgeR ASSIGN edgeR ASSIGN

updated 13.7 years ago • KJ Lim

periods (3h, 6h, 24h) vs. cells without ampicillin (0h). The control cells (without ampicillin) are log-phase, actively-growing cells. The amp-treated cells are persister cells that survive antibiotic treatment. We suspect...it's based on the assumption that most of the genes are not DE genes. so I worry that our case violates this assumption and would make the normalization not comparable acros…

qsmooth DESeq2 limma Normalization

updated 17 months ago • Xuan Yi

49-89-5160-5223 Mobile: +49-171-5169923 Email: r_hoffmann at mvp.uni-muenchen.de -----BEGIN PGP PUBLIC KEY BLOCK----- Version: PGP 8.0.1 - nicht f?r kommerzielle Nutzung lizenziert: www.pgp.com mQGiBEBiqn0RBADD7cwc5NHH98xZUn0hG53uL1nw2aVRXwurSWjqK5ytCUh2ZqB4...8VDwCgq/2PAsRp0rAX iXS1T2bL7Fow9zUAnAtzantYb0tV+Iw603AsKQjyDPBW =LGSI -----END PGP PUBLIC KEY BLOCK----- -------------- next part -----…

updated 20.2 years ago • Dr. Reinhard Hoffmann

status submission_date last_update_date 1 GSM1128470 NT2_2008216.1_1R01C01 GSM1128470 Public on Jan 06 2014 Apr 23 2013 Jan 06 2014 rownames(rt)<-rt[,1] #The first column as the row name rt<-rt[,-1] # pdata=rt > class(pdata...status submission_date last_update_date GSM1128470 NT2_2008216.1_1R01C01 GSM1128470 Public o…

normalization

updated 7.0 years ago • 15936296950

amp; 3 treatments. I have 6 biological replicates each per control/treatment. I've seen quite a few publications (BMC, PLOS one and others) that have aligned their reads to a reference transcriptome and then used RSEM or eXpress...the "Count-based differential expression analysis of RNA sequencing data using R and Bioconductor" publication online and in it is mentioned that in the case of no gen…

Sequencing GO Organism edgeR DESeq EBSeq Sequencing GO Organism edgeR DESeq EBSeq

updated 11.7 years ago • Nicole Ertl

expression profiling, genotyping, and mutation detection) are offered to pharmaceutical industries, public institutes, and clinics, and are adapted to preclinical and clinical trials. Job Opening: Ipsogen has a position available...amp;D and Oncogenomics activities -Participate in the interpretation of analyses -Participate in the publication and communication of data analysis results -Supervise…

Microarray Normalization Cancer Microarray Normalization Cancer

updated 19.2 years ago • Tagett Rebecca

then like to find the transcripts similar in both results and pull out the transcripts with the log fold change and p-values for both results. The log fold changes and p-values can be different between the to experiments

Microarray Microarray

updated 14.0 years ago • blockaa@huskers.unl.edu

the failure of 4 of my samples (out of 44) to normalise. <pre> rawC<-MRcounts(bt[,p],norm=FALSE,log=TRUE) normC<-MRcounts(bt[,p],norm=TRUE,log=TRUE) plot(x=rawC,y=normC,main=p)</pre> If p is a 'good' sample I see a sensible normalisation

normalization metagenomeseq

updated 9.8 years ago • Stephen Rolfe

relative intensities ranging from 0-1. I'm concerned that this is confounding my results, given the log fold change values that DESeq outputs are per unit of a continuous predictor. I've provided an example of my code for the...taxa (no adjusted p-values < 0.01), but the volcano plot reveals some odd behavior of the -log p-values that seem to plateau out at a certain ceiling below this …

deseq2 microbiome R

updated 5.3 years ago • greenm11

RG, method="normexp", > offset=100); > Corrected array 1 > Error in optim(c(beta, log(sigma), log(alpha)), > sumloglik, gr = grsumloglik, : > initial value in 'vmmin' is not finite We are working on this bug now. In the

limma limma

updated 20.7 years ago • Gordon Smyth

study-explorer/ ), and I obtain the following error: "ERROR: An error has occurred. Check your logs or contact the app author for clarification" Using a query from R (using an old chunk of code) gives another error: ``` library

recount recount3

updated 3.1 years ago • franceschini.gianmarco

<div class="preformatted"> Gordon, the M values for the Rquantile normalization are incorrect, the code is currently calculating M as M = M - E = (R - G ) - (qR - R) - qR is quantile normalized R channel, R and G are log channel intensities = 2R -G -qR Quick fix is to change the sign on line 61 of the code chunk : Rquantile = { R <- object$A + ob…

Normalization Normalization

updated 21.1 years ago • Marcus Davy

I am having problems with the installation of bioconductor. 1. Download the getBioC script 2. Log in as the user "R": cd ~R R > source ("getBioC.R") > getBioC("affy") It runs happily for a while, getting the versioning package, then

updated 22.6 years ago • Terry Therneau

BH") In the output of topTable if logFC is positive for contrast A-B does it mean it is log(A/B

limma logFC

updated 6.0 years ago • gv

whether the request is well formed XML or not. I've turned on logging, but nothing is written to the log file. Any hints on how to troubleshoot this situation would be appreciated. Best, Bastian [[alternative HTML version deleted

RWebServices RWebServices

updated 16.3 years ago • Bastian A.

So before I do a lot on my own, I was wondering (a) how best to upgrade AMI to 2.15.1 ( I can log in with SSH ) and (b) if the Rstudio interface will need to be reconfigured. Just thought I'd ask first. Thanks! Jeff [[alternative

updated 13.5 years ago • Jeff Knisley

effective size ( log2 fold change), I wanted to first use RNAseqPower to calculate the appropriate log fold changes. The instruction is pretty straightforward, however what I'm confused about is how to calculate coefficient

edgeR limma RNASeqPower

updated 4.9 years ago • Ahdee

geo/geo2r/?acc=GSE7621)>. I found the dysregulated genes in these sets by applying criteria log fold change is greater than 1.5 and p-vlaue < 0.01. My question is how to find the common dysregulated genes in these two

disease genetics micro array data microarray

updated 10.8 years ago • pankajnarula84

eBayes(fit\_counts\_cont) --- I have been able to decide the fit based on the p-value and the log fold change (see code below for a p-value of 0.01 and a lfc=1). But would also like to do this based on the B stats (lods). Is this possible

limma B stats decideTests

updated 10.8 years ago • Elsa

BPMAP file." [1] "Reading CEL Files & Extracting Intensities." [1] "Quantile normalizing/ log(2) transform." [1] "Finalizing data." Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent Tao Zhen Plant Functional

AffyTiling AffyTiling

updated 16.1 years ago • zhen tao

theory I understand what the intercept is, but I don't understand how this vector capture the mean log expression for the first factor (WT) if the value is the same for every sample. Where the information about the levels are

limma linear model intercept

updated 8.6 years ago • marconerdaum