Bioconductor Forum

the DKFZ? Full funding is provided for the duration of the PhD. **Application deadline is 15 May 2022** Find more information about the program at [https://www.dkfz.de/en/phd-program/index.html?campaign=phd/bioconductor

phd cancer genomics proteomics bioinformatics

updated 3.7 years ago • DKFZ International PhD Program

Antigenomic","Intronic"), lty = 1:3, bty="n") axis(1, xaxp=c(1,14,15), las=2) R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043) Matrix products: default locale

hta20transcriptcluster.db Microarray oligo

updated 3.6 years ago • Yang Shi

Hello! I went through the vignette and got all the errors sorted out, but I end up with odd-looking plots. I'm using three test samples, with a smaller BED file spanning only about seven chromosomes. I expected the colours to be similar to the plots shown in section 6.3 of the vignette, but instead the colours are scrambled all over, seemingly along the genomic position value? ``` par(mfro…

exomeCopy

updated 3.6 years ago • joel.wallenius

use the OUTRIDER package. Always when I try to run this code with MulticoreParam() I get an Error log: ods <- OUTRIDER(ods, BPPARAM = MulticoreParam(as.integer(8))) Error in serialize(data, node$con) : error writing to connection

RStudio R M1 BiocParallel Mac

updated 3.2 years ago • me.achleitner

and have a question on RMA from the affy package. It seems that the expression values are log transformed. Is there a way not to tranform it? Thanks very much, Yang --------------------------- Yang Tang Department of Neurology University of Cincinnati

updated 22.2 years ago • Yang Tang

counts appropriate for use as CIBERSORT input? It is said that the data used as input should not be log-space normalized 2. If VST is not appropriate how can I actually normalize the data appropriately? 3. Since it is declared

normalization r vst cibersort

updated 5.4 years ago • Matan G.

I am following the standard RNA-seq analysis workflow to make sense of some experimental data, using the DESeq2 package. Here is the MA-plot I have: ![](https://cdn.pbrd.co/images/Ha34sf3.png)I am not concerned about the low log-fold change, but this looks a bit weird, since I would have expected the major part of the genes to be found in the low counts...is the MA-plot I have: ![](htt…

deseq2 plotMA rnaseq logfoldchange

updated 7.9 years ago • ap_vc21

the same probe. The treatment of the duplicate spots can be very brief, e.g., just to say that log-ratios from duplicate spots were averaged before further analysis. I am particularly after papers in mainline biological

probe probe

updated 21.9 years ago • Gordon Smyth

to find an answer to this in the 'siggenes' vignette. Are the R-fold values that are calculated in log scale or not? I.e. if I have an R-fold value of 1.2 does that mean that the treated samples are 1.2x higher than the untreated

updated 19.9 years ago • Ettinger, Nicholas

makeProbePackage. But this function return the following error: "Expected but did not find the log-file hgu133atagprobe.Rcheck/00check.log after R CMD check" (bug??) So I let the check = FALSE, it's ok this time, but the constructed

updated 21.0 years ago • Yingtao Bi

Hi I am trying to do alignment and counting from a fastq file using package Rsubread. I am following the following instructions: http://combine-australia.github.io/RNAseq-R/07-rnaseq-day2.html However, every time I try to build index for the human genome the process is killed after 50% index is build and .files and .log are there but no .reads file is generated My code: buildindex(basename="…

rsubread buildindex fasta alignment

updated 7.2 years ago • writetoroopali

like to use a method which is able to filter the resultant list of differentially expressed genes by log fold change? Is there such a method and does it make sense to do this

microarray limma multiple treatments lfc

updated 9.7 years ago • brionyk9

about how different the expression it needs to be for it to count as 'changed'. I have tried using logs and ploting various graphs but i need to get some more exact info. any ideas? thanks

differential gene expression r commander

updated 9.8 years ago • milliesteward23

Is there a recommended way of extracting the log fold change when using scran's `findMarkers` function? I understand the reason why AUC is used here but AUCs is nothing that

scran

updated 5.7 years ago • ATpoint

The INSERM/Gustave Roussy laboratory “Apoptosis, Cancer & Immunity" (http://www.kroemerlab.com) is seeking a data scientist/bioinformatician to strengthen the computational capacities of the group. The post is located at the Centre de Recherche des Cordeliers in the historical center of Paris. You will work at the frontiers of scientific innovation, in the areas of cancer, immunology, met…

Genomics metabolomics biostatistics data integration Job

updated 10.2 years ago • David Enot

gt; As usual, please expect about 24 hours for these new versions to > propagate to the BioC public package repositories. Then install with > biocLite(). > > Cheers, > H. > > > Ben Madin wrote: >> G'day all, >> I don...gt; Ben > > -- > Hervé Pagès > > Program in Computational Bio…

Cancer RdbiPgSQL safe Cancer RdbiPgSQL safe

updated 16.7 years ago • Ben Madin

Hi all, I am trying to fit a burr distribution to my log transformed tpm values and have filtered these values to be above 0. Other distributions such as weibull, pareto runs...Hi all, I am trying to fit a burr distribution to my log transformed tpm values and have filtered these values to be above 0. Other distributions such as weibull, pareto runs fine

fitting parameter fitdistrplus burr

updated 3.7 years ago • melatoninixo

Dear ALL, i would like to use the function treat implemented in limma, in order to test simultaneously the test significance of my microarray linear model fit and my design. Because i have never used in the past, the argument fit in treat refers to the output of lmFit or from the ebayes fuction ? Moreover, if i would like to put an absolut log fold change > 1 i use lfc=1 ? And finally, i…

limma treat microarray bioconductor

updated 10.8 years ago • svlachavas

the __Genorm algorithm__ in the __NormqPCR package. __ So when I execute the selectHKs, should the log be TRUE or FALSE? I understand that Cq values are in the logarithmic scale so in my opinion it should be set to TRUE. Nevertheless

SelectHK qpcr Genorm

updated 7.7 years ago • jingchakvk

<div class="preformatted">Dear Bioconductor, I'm using EdgeR to find differentially expressed reads within 100bp windows. To help my analysis later on I'd like EdgeR to give me an output that contains every 100bp window I have regardless of if it's differentially expressed or not. I've attached a log of what I normally do to get differentially expressed read output. Any help on how to get …

edgeR edgeR

updated 12.4 years ago • Joanne.Lee@csiro.au

result of 6 different method for outlier: - Distances between arrays - Boxplots - Relative Log Expression (RLE) - Normalized Unscaled Standard Error (NUSE) - MA plots - Spatial distribution of M what is best criteria for

arrayQualityMetrics Microarray Outlier

updated 10.1 years ago • horcsct

the ratios range from <0 to >3. How can the GAPDH ratio be 0? Could these values represent log of the ratio? Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La Jolla

affy affy

updated 16.6 years ago • Lana Schaffer

is normalized or not. In the reference manual it is written that this number is the mean (log) reads across all samples of the specific group. 1) Are you referring to log2 or log10? 2) Were these values generated using

DiffBind

updated 4.8 years ago • roman.hillje

plotted, for example. Does the image plot depict both PM and MMMs or just PMs. Are the intensities log transformed? How is it constructed? Is it realted to the hist plot (which is just a histogram of the logged PM intensities

affy affy

updated 22.0 years ago • Stephen Nyangoma

information about: 1) SNP-ID 2) Sample-ID 3) Chr No. 4) Chromosome Position 5) Allele frequency 6) Log R Ratio I would appreciate if anyone could recommend a package/pacakges in Bioconductor that could analyze this kind

SNP SNP

updated 17.7 years ago • Tapan Mehta

of 0.  However, there are tons of germline mutations that are not filtered out, as the PureCN log files show.  Why is the private germline count 0?  I checked one sample's germline mutations manually to see if in

PureCN private_germline mutation_burden

updated 7.6 years ago • twtoal

Hi all, I'm trying to collect the datasets from public datasets from GEO. I found some data in fpkm and some in rpkm,tpm. My goal is to feed these data into a machine learning...Hi all, I'm trying to collect the datasets from public datasets from GEO. I found some data in fpkm and some in rpkm,tpm. My goal is to feed these data into a machine learning model

DESEQ2 fpkm rpkm tpm

updated 4.3 years ago • Sandhiya

is="" it="" lang="" mean?="" message:="" missing="" my="" nas="" needed="" of="" on="" pc="" piii="" public="" ram).="" research="" return="" ryals="" s="" section="" should="" statistical="" suite="" tel="" true="" university="" value="" warning="" what="" where="" works

updated 22.4 years ago • Lang Chen

Hi recently there has been some publication on the importance of GC and length bias ( Mandelboum et al, 2019, PLOS) . I'm looking into how to do this and came across

limma voom edaseq edger rnaseq

updated 6.1 years ago • Ahdee

div class="preformatted">Dear Sir/Madam, I am Mayur Doke persuing PhD in Public Health from Florida International University. I have read research article on Idiopathic and heritable PAH perturb

Pathways Pathways

updated 11.9 years ago • Mayur Doke

kind of normalization to run and how can I justify my choice in the method section of a submitted publication and in the defense?   Does Affymetrix has its own analysis and normalization software?  If so, where can

affymetrics normalization microarray

updated 11.0 years ago • Thomas.F.Hahn2

silly dream, but I want to create yet another gene set enrichment analysis tool. I am not keen on a publication, but on building a small community of creative and skilled developers in order to provide the research community

gene ontology go analysis gene set enrichment gene set analysis News

updated 8.4 years ago • ivozeller

I am doing a DE analysis comparing two strains, one wild type and one in which a repressor is overexpressed with 3. We expect that its downstream effectors will have very little expression and should come up as top hits in the DE analysis. We did the experiment in the presence and absence of drug and with 3 replicates per strain per condition. Without the drug, we see that all the counts for one …

DESeq2

updated 14 months ago • nicolettacommins

nbsp;    \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\# Begin Task Log \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#         \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\# End Task Log \#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#\#  __  &a…

limmagui shiny

updated 9.8 years ago • christopher.clarskon15

<div class="preformatted">Thanks James, but I did do data <- as.matrix(data) before running lmFit, and is.matrix(data) returns TRUE. ("data" is just for illustration purpose, but thanks for pointing out the variable name issue.) Any other suggestions? Yiwen -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Wednesday, April 06, 2005 2:51 PM To…

Microarray Cancer limma Microarray Cancer limma

updated 20.8 years ago • He, Yiwen NIH/CIT

Hi, based on DESeq2 result, I ranked all genes based on sign(lfc) \* log (p-value), and ran GSEA prerank based on the ranking. Some gene sets highlight the difference between my experiment groups...lt;- counts_all_deseq2[rownames(counts_all_deseq2) != "",] mat_set <- counts_deseq2[geneset2,] #log transform of raw counts mat_set.pca <- prcomp(log2(t(mat_set)+1),center = TRUE…

deseq2

updated 8.2 years ago • Raymond

featureCounts(object), locfunc, : every gene contains at least one zero, cannot compute log geometric means > head(dxd) class: DEXSeqDataSet dim: 1 154 exptData(0): assays(1): counts rownames(1): ENSG00000000003:E001...cts <- counts(dxd) geoMeans <- apply(cts, 1, function(row) if (all(row == 0)) 0 else exp(mean(log(row[row != 0])))) idx <- which.max(colSu…

DEXSeq DESeq2 dexseq deseq2 alternative splicing

updated 10.3 years ago • Fahmi Nazarie

created a PCA plot for our RNAseq count dataset following the instructions in the vignette, using r log transformation. Though my plot got generated, I got this warning message when I called the rlog function: ___Warning message...of this. We recommend instead using the varianceStabilizingTransformation or shifted log (see vignette).___ So if I understand this correctly, in genes with sum of…

deseq2 pca rlog transformation variancestabilizingtransformation

updated 9.7 years ago • Shobana Sekar

as.matrix(raw$V3), gi) iset1$totals <- colSums(assay(iset))</pre> The I use the average log-CPM corresponding to a count of 5 to filter out pairs of bins prior to differential analysis with edgeR. <pre> ave.ab...lt;- filterTrended(iset) #plot it smoothScatter(trended$log.distance, trended$abundances, xlab="Log-Distance", ylab="Normalized abundance") o <…

diffhic edger

updated 9.1 years ago • andreucat91

proximity to numerous other top-notch medical and research institutions including Harvard School of Public Health, Massachusetts Institute of Technology (MIT), The Broad Institute of MIT and Harvard, Boston Children’s Hospital...and how such variation influences human health and disease. Read more about our research, recent publications, and software here: http://pinellolab.org **Requireme…

CRISPR SingleCell Genomics

updated 4.3 years ago • lpinello

integration of the wealth of experiments that have already been performed and are available from public databases. We collected, from the public microarray repositories GEO1 and ArrayExpress2, over 9000 raw data files...the Gene Expression Atlas2. This project aims at implementing, based on the current prototype, a public interface for the Human Gene Expression Map. Through this interface, user…

Microarray Annotation Visualization PROcess Microarray Annotation Visualization PROcess

updated 16.2 years ago • Gabriella Rustici

<div class="preformatted"> Excellent criticisms! I'm happy that you are willing to answer them in detail, and look forward to a piece-by-piece description of how we can improve! I'm not joking, and I'm not being snide. This is a manpower issue, and having worked with open source projects nearly as long as Eric, can hardly help but agree with him. Documentation, for which we do better th…

GUI Cancer GUI Cancer

updated 21.9 years ago • A.J. Rossini

given the count data and just the fact that with normalized counts I am getting completely different log fold changes for results as well as base mean results. The issue I am having is as follows: I already have some data that suggests...But just to be sure that it is alwayts with respect to the first contrast.. so for example, any log fold change means that much log fold change in normal com…

DESeq2 logfoldchange counts

updated 7.0 years ago • A

<div class="preformatted">Dear limma experts, I am analyzing the data set given to me and described by these the column names of my MA object: > colnames(MA.hyp) [1] "../ampcon/mev/C0-_1stround_vs_C60-_1stround_13263536.mev" [2] "../ampcon/mev/C0-_2ndround_vs_C60-_2ndround_13263534.mev" [3] "../ampcon/mev/C60-_1stround_vs_C0-_1stround_13263533.mev" [4] "../ampcon/mev/C60-_2ndround_…

limma limma

updated 19.5 years ago • Andrew Mcdonagh

have the time Sean (or >someone else) I would be very grateful. > >Yes, the M-values are log, but I have checked and I do not have any >infinite or NaN values in the matrix. > >I have som questions regarding hclust...gt; >/ A very confused person > > > > >>>I assume that the M values are a log, so yo…

Clustering Clustering

updated 22.2 years ago • Marcus

Hi, hoping one of the Gviz team can help me with this (mostly so I can thank you for the really flexible package!). Example data: cpgGR <- makeGRangesFromDataFrame(data.frame(chrom = c(1,1), start = c(23884842, 23885682), end = c(23885087, 23886212))) ids <- c("CpG:23", "CpG:49") cpgTrack <- AnnotationTrack(cpgGR, id = ids, name = "CpG…

gviz-package gviz annotation

updated 8.8 years ago • bruce.moran

For example a simple difference in means would obviously not be a problem for quantile normalization. Nor would a simple difference in variance. These and more complicated differences between distribution can be accounted

Normalization Normalization

updated 21.8 years ago • Leslie Cope

slide design/spatial info (amenable to be used with this kind of raw input data - e.g., neither .CEL nor Illumina input data)? my R version - attached packages: > sessionInfo() R version 2.4.0 Patched (2006-11-25 r39997) i486-pc-linux

Microarray probe affy affyio Microarray probe affy affyio

updated 18.0 years ago • Teresa Colombo

Dear Maintainers As announced earlier this year, Bioconductor is moving version control systems from SVN to Git. ## The plan --- * Software, experiment data, and workflow packages will be maintained as git repositories created to capture the full commit history of each package. (the commit history of the 'data\_store' portion of data experiment packages will unfortunately not carry forward …

git svn infrastructure bioconductor News

updated 8.5 years ago • nitesh.turaga

a", 5), rep("b", 5))) #compute normalization factors s <- c(values_a, values_b) / exp(mean(log(c(values_a, values_b)))) #fit negative binomial glm - EDIT: This is wrong, see first answer res1 <- MASS::glm.nb(log(counts) ~ condition...data = example) mu1 <- exp(res1$fitted.values) * s #fit model without log res2 <- MASS::glm.nb(counts ~ condition, data = e…

deseq2 design matrix

updated 7.0 years ago • nikosbosse

warnings produced by corfit=intraspotCorrelation(MA, design) ... Warning message: NaNs produced in: log(x) Warning message: NaNs produced in: log(x) Warning message: NaNs produced in: log(x) Warning message: NaNs produced in: log(x) &gt

limma limma

updated 17.4 years ago • Pie Muller

I downloaded the goslim_generic.obo from geneontology.org and followed the post: https://support.bioconductor.org/p/128407/ to slim my GO BP terms. However, one GO term: GO:0002831 was not counted. What could be the problem here and any recommendations on how to address it? ```r ids<- "GO:0002831" myCollection <- GOCollection(ids) slim <- getOBOCollection(goslim_generic.obo)…

GO.db GOslim

updated 2.1 years ago • amanda

lt;19>::Proxy)’ is ambiguous PrebuiltXPtr curbuilt(prebuilt[r]); R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Oracle Linux Server 7.9 Matrix products: default BLAS: /project

SimpleR

updated 2.9 years ago • cisbio

packages/3.16/books/src/contrib/PACKAGES' Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt) Installing package(s) 'dada2' Warning: unable to access index for repository https://bioconductor.org/packages

dada dada2

updated 2.9 years ago • elliottchon97

dataset and then combine them using ComBat or Limma or combine them first and then normalize and log transform. Additionally, I would like to perform differential expression analysis and gene set enrichment analysis

RNASeqData DESeq2 Normalization

updated 18 months ago • Tanvi

to normalize the data xn <- normalizePlates(x, scale="multiplicative", log=FALSE, method="Bscore", varianceAdjust="byPlate", save.model=TRUE) The function call takes very long. In my case with 100 plates

cellHTS2 Normalization

updated 4.1 years ago • liebi83

Hi, I have used Voom to transform my data with the TMM scaling factor and identified a list of differentially expressed genes for my RNA-seq data. What I want to do next, is to generate a bar plot on some genes of interest and also plot an expression heatmap. My question is, can I use the transformed E values from ```Voom``` for this, or should I recalculate the Log2CPM values using the ```cp…

edgeR limma

updated 2.3 years ago • petertam1343

do an MDS plot on the input count matrix, all looks "normal". When I do the same plot on the output log CPM matrix (E), the samples (N=329) cluster strongly into two groups of about equal size. This happens no matter how I run voom

RNASeq RNASeq

updated 12.5 years ago • Ina Hoeschele

documentations I have followed resulted in densities that are similar across all sample and roughly log-normal distributed. If I plot the logCPMs' densities before and after the transformation I still get muti-modelus DIFFERENT

limma

updated 4.8 years ago • Omar Elashkar

class="preformatted"> Hi, I have high through array data with two peaks in its distribution (raw and log 2 transformed). I googled it looks like is mixed Gaussian distribution - two normal distribution as some people suggested

limma convert limma convert

updated 12.1 years ago • Guest User