Bioconductor Forum

IS Project Manager/ Day/ 40 Hrs/ Channing Division of Network Medicine - (3133887) Description This position includes both project management and advanced software development. The successful applicant will perform multidisciplinary work in data science, clinical trials, and cloud computing. Our group is centrally involved with the Bioconductor project, a 20-year open source/open development…

softwaredevelopment Job job cloudcomputing genetics

updated 5.0 years ago • Vincent J. Carey, Jr.

<div class="preformatted">I am running into memory limits and have been unable to write the correct code to increase the allocation size. Below is my output. I am currently running Windows XP with 2 GB of RAM. Windows Task Manager tells me that I have over 1GB of physical memory free so I should have plenty of room to increase. > memory.size(max=T) [1] 126066688 > memory.l…

updated 21.4 years ago • Kimpel, Mark W

I am using clusterProfiler to check whether a group of genes of interest is enriched in genes coming from a term from a custom ontology. I am following the outline provided by this article: "use clusterProfiler as an universal enrichment analysis tool", http://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/ The problem is that I run into an error: &…

clusterprofiler gene ontology

updated 7.4 years ago • anton.kratz

<div class="preformatted">Hi, There is a new paper out at BMC bioinformatics that seems to justify the use of filtering before differential expression analysis is performed...div class="preformatted">Hi, There is a new paper out at BMC bioinformatics that seems to justify the use of filtering before differential expression analysis is...filter out the control genes before testing. I w…

Cancer Cancer

updated 17.1 years ago • Daniel Brewer

<div class="preformatted">Hello, Sorry that I bring up this again, but I do want to know if my logic is correct or not, with regard to subset a big data set according to different research questions and start from normalization to set up different design matrixes and contrasts. I am particularly unsure about the 2nd question of comparing normal and tumor type I (AR+), and how pairing and b…

Normalization limma Normalization limma

updated 11.6 years ago • Rao,Xiayu

lt;- readData(NORM.data, factor = PHENO) BATCH.data <- ARSyNseq(BATCH.cor, factor="Group", batch = FALSE, norm = "n", logtransf = TRUE) to remove batch effect it separates the samples on PCA . But when is use varFilter(BATCH.data...i get more number of DOWN DEG than UP DEG after performing eBayes. Is there any other simple batch correction and gene filter package availabl…

DGE limma

updated 23 months ago • Amit

<div class="preformatted">Dear All, I have been downloaded the SAGEnhaft library an start to learn about it. I get the paper, as well. But, I am very confusing if I will need another software, eSAGE, SAGE2000, or another one, to do all post analysis on...Dear All, I have been downloaded the SAGEnhaft library an start to learn about it. I get the paper, as well. But, I am very confusin…

SAGE sagenhaft SAGE sagenhaft

updated 19.4 years ago • Marcelo Luiz de Laia

Dear All I generated a an OrgDb package for Salmo salar, using \`AnnotationForge::makeOrgPackage()\`. However, the sqlite table REFSEQ (containing RefSeq IDs) is missing when I load the package <pre> libarary(org.Ssalar.eg.db) columns(org.Ssalar.eg.db) [1] "ACCESSION" "CIGENE_ID" "GENENAME" "GENE_BIOTYPE" "GID" </pre> But looking into the .db I can see the table is th…

annotationdbi

updated 9.4 years ago • Fabian Grammes

I am trying to use motifstack in bioconductor. I was wondering if there is any way to reduce the size of yaxis or limit the yaxis to a maximum value. I tried to use plotYaxis but I am unable to reduce the size of the yaxis. I was

motifstack plotMotifLogoStack

updated 6.5 years ago • saadmurtazakhan

<div class="preformatted">Hi I have a group of samples for which I'd like to ascertain if differential binding is detectable based on a "condition" binary variable (stored in DBA_CONDITION). However, these samples have been processed in 4 batches (each batch has at least 3 samples). I would like to run a multifactorial analysis to regress the batch effect first, and then possibly analyse…

updated 11.7 years ago • Giuseppe Gallone

from 35 patients (myData). I have 3 different Tissue Type (TT1, TT2, TT3) and I saw that there was a batch effect due to the technician that did the experiment. As some of my patients have only 1 sample at the moment I am not using...I used the following code: dds <- DESeqDataSetFromMatrix(countData = myData,colData=batch[,c("Sample_ID","Tissue_Type","Technician")],design = ~ Te…

deseq2 rnaseq

updated 9.8 years ago • ldetorrente

Affymetrix data? I have a 2 x 2 design, treatment versus control at two labs. There are strong (lab) batch effect that can be seen by clustering the data. So far I have computed RMA (and GCRMA) values for each lab separately, normalized...expressed genes via lmFit, eBayes and TopTable. I would like to estimate how much of a batch effect remains. >From my numeralogist roots, I know that a…

Clustering Clustering

updated 21.1 years ago • Malard, Joel M

div class="preformatted">Hi I am working with single-channel Agilent data. I have two batches of microarrays for biopsies from different patients (batch 1, 25 arrays; batch 2, 34 arrays). There are no replicate samples...batch effect. Initially, I tried removing the batch effect using METHOD 1. Using this method I found I was getting 1000s rather...on what I'd seen on analyses with the batch…

updated 13.6 years ago • Hoyles, Lesley

div class="preformatted">Hi, I was exploring batch effects in my data. At this stage, I don't want to introduce the 'variable of interest' (i.e. 'cancer' in the vignette/example...function (and get combat_edata2)? Will this correctly reflect the expression data corrected for batch effects? ###### Code ##### library(sva) library(bladderbatch) data(bladderdata) library(pamr) library(limma) p…

sva sva

updated 13.9 years ago • Tim Smith

Dear Bioconductor community, I encountered a difficult problem in correcting for batch effect in repeated measurement data, which has troubled me for a long time. This is not an experimental design usually...by years elapsed between 2 visits) to assess this 'variability'. However, there seems to be some batch effect as shown in the PCA plot below: ![PCA plot for vst normalized counts][1] …

miRNA BatchEffect RNASeq limma

updated 2.3 years ago • Wending

div class="preformatted">Hello, What limits the number of sequences and size of sequences that are part of a DNAStringSet? Are there any way to change these limits? On my home laptop I can create a DNAStringSet...of twenty thousand sequences. Does anyone know what is creating this difference is maximum size? Is there any way I can "up" the amount of memory available to a sequence set? I …

updated 15.7 years ago • Erik Wright

246, 246)">quantitation) and I need to setup a condition table for running DESeq2</span> <span style="background-color:rgb(246, 246, 246)">in RStudio.</span> <span style="background...please take a look to this&nbsp…

deseq2 multiple comparisons

updated 10.7 years ago • annalisa.giampetruzzi

I am attempting to plot data where the groups are not the same size. The example argument for using groups is: > plotTracks(dTrack, groups = rep(c("control", "treated"), + each = 3), type = c("a", "p", "confint"))&nbsp...nbsp; Does anyone know how to plot with groups that are different sizes

gviz R granges

updated 10.0 years ago • drummerz

div class="preformatted">Dear Group, table(Rle) seems to ignore empty levels. x = Rle(c(2,3,1,2,3,2),rep(2,6)) levels(x) = as.character(0:5) table(x) table(factor(as.numeric(x),levels

IRanges IRanges

updated 13.3 years ago • Peter Haverty

https://support.bioconductor.org/p/92753/ In his case, subject and batch are identical, so "There is no need to do any batch correction. The baseline differences between subjects, including any...batch effect, is already accounted for in the paired analysis." <pre> group <- factor(c("wt","wt","wt","ko","ko","ko")) subject <- as.factor(<span...style="background-color:Yel…

edgeR paired samples batch effect

updated 7.4 years ago • NGS-seeker

preformatted">Hello, I have a question concerning hierarchical clustering and the effect of group sizes. I would like to select genes that are differentially expressed between group A and group B. Afterwards, I wish to cluster...the samples by these genes. In principle, it works fine, but I have a problem if the group sizes are significantly unequal. One example is as e.g.: group A: 53 sampl…

Clustering Clustering

updated 20.1 years ago • Heike Pospisil

I have a naive question, Even though I've seen a lot of question regarding this issue (batch effect) in RNA-Seq analysis. I still don't understand exactly what EDGE-R is performing during this procedure. For example...nbsp;           rep("Mutant",3))) and create a batch factor: batch <- factor(c("…

R edger batch effect

updated 9.1 years ago • kaihami

DE between a gene in a case and control, however, there are two underlying teams (A and B) (the experiment was run in two batches) so I would like to consider them as well.  the data format is sth like below and I have made...sure, "condition" and "team" are factor <table border="1" cellpadding="1" cellspacing="1" style="width:500px"> <tbody> <tr> <td>gene_in_sa…

deseq2 block pca

updated 9.7 years ago • akp

TMM normalization is appropriate for my data. I apologize for this long winded email. I am not a trained bioinformatician and therefore have been struggling with some data analysis. A colleague and I did an RNA seq experiment...at 3 different time points. I know that this is not an ideal experimental set-up, we did this experiment 3 years ago. We used the Trinity package to do most of the trans…

Normalization edgeR

updated 11.5 years ago • Ni Feng

div class="preformatted">Dear List, We have performed a high-throughput rtPCR experiment for selected 120 genes on 2,000 human subjects using TaqMan platform. There are two batches/runs, and three housekeeping

Microarray Microarray

updated 12.7 years ago • shirley zhang

Hi all, I have the following type of data: - 5 batches (5 different data sets) - 2 conditions (wt, mutant) - 3 different tissues (data 1 and 2 represent tissue 1, data 3 and 4 represent...Hi all, I have the following type of data: - 5 batches (5 different data sets) - 2 conditions (wt, mutant) - 3 different tissues (data 1 and 2 represent tissue 1, data 3 and 4 represent tissue 2, data 5 repr…

DESeq2

updated 4.2 years ago • Ela__77

to Statistical Analysis and Programming in R* EMBL Heidelberg, 28-29 March 2010 - Computer Training Lab This course is addressed at beginners with some experience in programming who want to learn using R for the analysis...t Wien Dr. Theresa Scharl, Technische Universit?t Wien und Universit?t f?r Bodenkultur Wien Time table: Monday 29-03-2010 09:00 - 10:30 Introduction to R I Break 11:00 - 12:…

Classification Classification

updated 16.1 years ago • Wolfgang Huber

error using the function flow_auto_qc: ```r >fs #fs is my flowSet object A flowSet with 283 experiments. column names(22): FSC-A FSC-H ... FJComp-PerCP-Cy5-5-A Time >fs.ai<-flow_auto_qc(fs, remove_from = "FS_FM") Quality control...for the file: AAM_d7_CD19 + 'Error: cannot allocate vector of size 856.3 Gb.' ``` Do you know if there are compatibility issues between flow…

flowAI

updated 2.6 years ago • Simoluc

class="preformatted"> Hello, I have a question regarding a design, in which there is a factor for "batch effect". I understand how to get the p-values when taking in account the batch factor. I wanted to ask whether it is possible...to obtain also the actual counts after batch effect removal. Thanks a lot, Gilgi -- output of sessionInfo(): none -- Sent via the guest posting facility at …

updated 12.1 years ago • Guest User

Hi, In the Nat Prot paper about Ballgown, it's said as follow: _Note that Ballgown’s statistical test is a standard linear model-based comparison...For small sample sizes (n < 4 per group), it is often better to perform regularization. This can be done using the limma package in Bioconductor._...And second, how should the step(regularization) be taken during the ballgown procedure as thi…

limma rna-seq

updated 8.3 years ago • zoukai3412085

<div class="preformatted">Hi All I am interested in downloading the Breast cancer data from Zhao et al from SMD. I have used the following two commands before to download SMD data before Library(limma) G = read.maimages(dir(pattern='*.xls'), source='smd', fill=TRUE,sep='\t') RG = read.maimages((dir(pattern='*.xls')),columns=(list(Rf=Ch1 Intensity (Mean),Gf=Ch2 Intensity (Mean),Rb=Ch1 I…

Cancer Breast Cancer Breast

updated 21.8 years ago • Ian Jeffery

HI everyone, I'm running DESeq2 to identify genes that are differentially expressed between two general phenotypes: fruits and vegetables. Here's my design: ```r general specific batch =============================================== 1 fruit apple apple 2 fruit apple apple 3 fruit pear pear…

DESeq2 deseq2

updated 4.6 years ago • Ania

or tissues? This would probably prove useful to you - I've played around with it, and ~450 of their training set probes are on the 450k. You can email the authors for their code. http://www.biomedcentral.com/1471-2105/13/86/abstract...is probably technical artifacts. I think its unclear what these effects do (if anything). Effect sizes less than 1% (which get published) are probably less likely …

updated 13.5 years ago • Andrew Jaffe

Hello everyone, I'm working with an RNAseq (bulk) dataset and I need to correct the batch effect induced by days of experiment (showed also by MDS plot) I have two genotypes (APOE and C57) and each has been processed...APOE_Day1 - APOE_Day2 - C57_Day3 - C57_Day4 I need some suggestion on how to model this batch effect in the design matrix in order to find difference among C57 and APOE …

BatchEffect edgeR

updated 2.4 years ago • Giuseppe

I have completed multiple RNAseq experiments using a targeted approach (custom Illumina panel looking at only genes of interest). I followed each run by salmon...I opted for "lengthScaledTPM" in order to address the transcript length and library size. My first run only included 12 samples and my last included 48 which further encouraged me to use the "lengthScaledTPM...for this study (the second …

tximport RNASeq salmon

updated 3.0 years ago • Ivana

I'm adjusting for batch effects in 450K data using ComBat in the sva package. When I run ComBat, I get the following error: > batch = factor(pheno...gt; modcombat = model.matrix(~1, data=pheno) > methCombat = ComBat(dat = as.matrix(meth), batch = batch, mod = modcombat) Found7batches Adjusting for0covariate(s) or covariate level(s) Found216170Missing Da…

microarray combat sva batch effects

updated 6.2 years ago • anne.bozack

<div class="preformatted">Dear Colleagues, The Department of Biomedical Informatics at the University of Pittsburgh has at least one post-doctoral position available with funding from the National Library of Medicine. I invite bioconductor colleagues to apply or circulate as you see fit. Contact Toni Porterfield if interested. Detailed information follows below my signature. Roger Day Uni…

Cancer Cancer

updated 14.0 years ago • Day, Roger S

Hi! I'm new to RNAseq analysis and had a few questions in regards to batch effects. 1) I have RNAseq data for two conditions obtained from two different batches that I am trying to analyse. I have...included batch as a covariate while creating the DESeq object, but I am not sure if I am supposed to remove batch effects using limma, etc...for it in the DEseq object is enough. 2) When doi…

DESeq2

updated 13 months ago • A

Biotechnology Center at the University of Illinois Urbana-Champaign. We are hiring a new analyst and experience in any area of ‘omics data is fine. We will also consider those with lesser experience but the ability to learn on...the job through in-house training. See the full job posting and application site at https://illinois.csod.com/ux/ats/careersite/1/home/requisition

Metagenomics GenomicVariation Genomics RNASeq ChIPSeq

updated 3.6 years ago • Jenny Drnevich

genes between the two conditions using DESeq2. This is the script I am using to read my raw count table into DESeq2: featureCountTable <- read.table("featureCountTable_RawCounts.txt", sep="\t", quote=F) colData <- data.frame...a warning: Warning messages: 1: In log(ifelse(y == 0, 1, y/mu)) : NaNs produced 2: step size truncated due to divergence So again I have tried…

RNASeq DESeq DESeq2 RNASeq DESeq DESeq2

updated 11.7 years ago • Assa Yeroslaviz

It seems next to impossible to change the size of the `geom_text()` labels with `autoplot()` in *ggbio*. For example, take the reproducible code: require(ggbio) require(GenomicRanges...ibb.co/yyTCyKy"><img alt="sss" border="0" src="https://i.ibb.co/r6Ph6q6/sss.png"/></a> The label sizes are too small. So, I figured that something like this would work: p + geom…

ggbio annotation

updated 6.5 years ago • Kevin Blighe

Proteomic Data", as part of the Molecular Phenotyping to Accelerate Genomic Epidemiology (MOLPAGE) - Training WorkPackage Series. Coordinators: Luisa Bernardinelli and Carlo Berzuini Dates: 26-30 March 2007 Location: Pavia

updated 19.1 years ago • Brian D M Tom

Hello, I'm doing some bulk RNA-Seq analysis to identify different genes in two condition (Braccio) but before that I want to identify some not known variable and delete the batch effect (RIN) of my variable. So I'm moving in this way: ```r dds_campione <- DESeqDataSetFromMatrix(countData=raw, colData=condition_breakfast, …

DESeq2 BatchEffect sva

updated 24 months ago • michelafrancesconi8

analysis of "mass spectrometry" data (Max-quant- Intensity values) by using DEP package. I have a batch effect on my data. Is there any way to take care of the batch effect in DEP package (https://www.bioconductor.org/packages...devel/bioc/vignettes/DEP/inst/doc/DEP.html). I know there is a batch server that takes care of such a problem but i'm looking for something within the package. Can you pl…

Proteomics DEP MassSpectrometryData

updated 4.6 years ago • barrypraveen

differential expression for (eg. TP1 & TP2). However 11 of these patients are in one sequencing batch (B1) and the remaining 9 are in another batch (B2). In DESeq2 Vignette in the section "Model matrix not full rank" there is a part...how you can control for this type of situation. I have tried applying the design matrix as follows: (batch + batch:ba.pi + batch:condition) where ba.pi is t…

deseq2 sva combat

updated 6.5 years ago • ege.dedeoglu

makeTxDbFromUCSC(genome = 'mm10', ```` tablename ``<code> = "refGene")<br/> Download the refGene table ... OK<br/> Download the refLink table ... Error in normArgTable(value, x) : unknown table name 'refLink'</code> Do you know what the problem

genomicfeatures maketxdbfromucsc refseq

updated 9.6 years ago • Sebastien Vigneau

a gene of interest). The issue is that library prep for 16 cell lines wasn't performed in the same batch. We performed library prep for 8 cell lines (equal distribution between control and knockdown) and then performed another...batch" of library preps for next 8. The library prep method was the same. They were sequenced on the same sequencing run. My question...is, while running DESeq2, shou…

DESeq2

updated 5.3 years ago • dhwanirupani92

<div class="preformatted">Dear Serge, That's what I do. For example, the time course analysis in Peart, M. J., Smyth, G. K., van Laar, R. K., Richon, V. M., Holloway, A. J., Johnstone, R. W. (2005). Identification and functional significance of genes regulated by structurally diverse histone deacetylase inhibitors. Proceedings of the National Academy of Sciences of the United States of A…

Microarray Cancer limma Microarray Cancer limma

updated 18.6 years ago • Gordon Smyth

grip of is the comparability of the B statistic numbers generated. Is a value of 6 for a gene in one experiment directly comparable to a value of 10 for the same gene in a different experiment? One other question I had was on...change of log fold change 1 would be 10 in reality? Is this the same as the M value given in the top table lists? We are also working with some more complex experimental …

updated 21.6 years ago • Elizabeth Brooke-Powell

<div class="preformatted">Pete, Thanks for the bug report. This is fixed in IRanges 1.17.11. Note that the data inside the rle must be a factor. Adding levels to an Rle after the fact doesn't create a factor-Rle. x = Rle(c(2,3,1,2,3,2),rep(2,6)) levels(x) = as.character(0:5) This is a numeric-Rle with no levels. > x numeric-Rle of length 12 with 6 runs Lengths: 2 2 2 2 2 2 …

IRanges IRanges

updated 13.3 years ago • Valerie Obenchain

gt; mMat = model.matrix(~as.factor(cancer), data=pheno) cbMat = > ComBat(dat=as.matrix(hmMat), batch=pheno$plate, mod=mMat, > par.prior=TRUE, prior.plot=F) Found29batches Note: one batch has only one sample, setting mean.only...TRUE Adjusting for1covariate(s) or covariate level(s) Error in ComBat(dat = as.matrix(hmMat), batch = pheno$plate, mod = mMat, : The covariate is c…

#combat

updated 7.0 years ago • sharvari gujja

__ __<http://www.journals.elsevier.com/international-journal-of-approximate-reasoning/call-for-papers/special-issue-on-statistical-and-computational-methods-for-g/>   __Background and Scope:__ In the last decade, the...be also considered, as data have very high dimension and computational resources are limited.   Papers are sought on theoretical and practical…

news call News

updated 10.5 years ago • rancoita.paola

I am tempted to use SVA for removing batch effects from two different technologies from which I get counts data for miRNA. The data do not have common reference...different treatment in both technologies).  I understand concept of batch effect (days, reagents, technicians etc ...)  BUT am I allowed to use SVA if 2 different technologies were used to get these

normalization deseq2 sequencing sva

updated 10.7 years ago • marcin.bazyliszek

I am using `plotPCA()` function to create the PCA plot, but I do not know how to change the dot size. Code as follwing: ```r plotPCA(rld, intgroup = "Tissue") ``` ![enter image description here][1] Does anyone know how to change the dot...size? I want it smaller. Thank you for your help in advance:) [1]: /media/images/13f3e1e9-f390-47f1-a023-b0b26257

plotPCA PCA

updated 3.0 years ago • Yijing

Hello- I am doing differential network analysis. However; I have different sample sizes for the different conditions. I am observing that since I am using Pearson's correlation in wgcna to measure the weights...the weights of correlation depend on the sample size( where larger samples created lower weights). Since I am calculating different centrality measures individually- to...networks -- I …

coexpression WGCNA

updated 5.0 years ago • Hanna

<div class="preformatted">I am unsure how to interpret the M-value produced by limma topTable when analyzing a multi-factoral, multi-level experiment. As an example, suppose I test one gene under the same 2 conditions (1 and 2) in two different experiments (A and B). The mean expressions in the two experiments are very different but in both cases condition 1 has higher expression levels th…

limma limma

updated 20.4 years ago • Kimpel, Mark W

I performed a SAM (Significance Analysis for Microarray) analysis in R, and retrieved the delta table with the corresponding # of false positives, positives, FDR...etc for each delta. In that table, it also contains the columns

updated 15.7 years ago • Casper Shyr

include Sentrix_position with Batch but not sure how combine two variable here? library(sva) > #phenotype file > sample.info <-read.table("Sample.Info.csv...lt;-sample.info[,1] > > head(sample.info2) Sentrix_ID Sentrix_Position Batch Recruitment Category Gender eGFR DC541 2.03e+11 R06C01 Batch 15 US Co…

Epigenetics combat EPIC

updated 3.0 years ago • Jitendra

nbsp; If I call the help function for Combat, I get the information :   ComBat(dat, batch, __mod__, numCovs = NULL, par.prior = TRUE,   prior.plots = FALSE)   <table border="0" cellpadding="0" summary="R argblock"> <tbody...p> </td> <td> <p>Model matrix <strong>for outcome of interest</strong> and other covariates besides …

ComBat

updated 11.3 years ago • maren.lang

div class="preformatted">Hello you, i have a problem using Rankproduct: I read the papers of Rainer Breitling and the Rank Product Vignetes but still have questions about this method 1. I tried to calculate...the Rank product in Excell (as explain in the paper of Rainer Breitling) using a small data set, i didn't get the same results as calculating it with R-Programm. Can somebody...Rankprod…

updated 20.0 years ago • Nadine Ketchandji