Bioconductor Forum

dds) # lists the coefficients res <- results(dds, name="condition_trt_vs_untrt") # or to shrink log fold changes association with condition: res <- lfcShrink(dds, coef="condition_trt_vs_untrt", type="apeglm") ``` In the above

deseq2

updated 5.8 years ago • megapode32559

However, in my otu table, there are zeros in almost each column, which prevent DESeq to do the log transform. I noticed that if I just simply add 1 to all values, I can bypass the issue. But there are several discussions indicating

deseq2 input files zero

updated 8.4 years ago • yanmin

datasets. However for few probesets I get negative intensity values. I understand that the data is log transformed but is there any way to avoid  that and get the intensities on a linear scale without any negative values

normalization scan.upc

updated 10.8 years ago • sanj

pipeline works well.The problem is I am trying to draw dashed lines in my graph showing the -2 and 2 Log cutoff, and the significant genes in red points instead of black ones. Does anyone knows how to do these? Thanks Pablo

MA Plot

updated 10.7 years ago • pablo_calza

<div class="preformatted">Dear all, Maybe this is a stupid question but... Is there a general assumption about the way the highest expression values of a gene (/all genes?) in a series of chips would be, such as log normal, normal...? I know that there are some outliers in these part of the spectrum but what else if they are excluded from analysis...way the highest expression values of a …

updated 21.3 years ago • Phguardiol@aol.com

MA list is composed of M, A values. If i wanna go for the analysis of my data, i need to have the log ratios of all the probes. Kind regards, -- Raju Kandimalla, PhD student Erasmus MC Department of Pathology JNI,Room H Be-302

GO convert GO convert

updated 17.2 years ago • r.kandimalla

<div class="preformatted">Hi, I was hoping that someone might be able to help me. I have inherited data from 4 Agilent arrays. I would like to recover and output to file the normalised signal intensity of the Cy3 and Cy5 data if possible, rather than the log ratio of each. If anyone can suggest a way to do this I would be most grateful. As the MA can be use by plotDensities() to show the.…

updated 15.7 years ago • Lloyd, Bryony

I came across the function "normalizeMedianValues(x)" in Limma. In my case my matrix x contains the log transformed intensities where each column is a different sample (in this case patients) and each row is a different protein

median normalisation intensity data Limma

updated 5.4 years ago • sandra.murphy

Is it possible to calculate a confidence interval on the log fold change reported in the output of edgeR? I suppose that knowing the number of reads in a gene and the tagwise dispersion

edgeR statistics confidence interval

updated 9.8 years ago • ri.lars

Dear, I would like to determine summit value for a list of enhancers from a public database. I use these lines: ```r # load features table: 3 columns Chr, Start, End features <- read.table("GeneCards_GeneHancer

DiffBind

updated 5.0 years ago • mdidish

for your understanding! Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109

Cancer Cancer

updated 16.3 years ago • Hervé Pagès

to know what parasite genes are expressed in the infected tissue. Is it possible to do so? Related publications are highly appreciated. Best, Xinxia </div

Microarray oligo Microarray oligo

updated 20.0 years ago • xpeng

div class="preformatted"> The Bioconductor core team would like to publically thank James MacDonald for his recent testing and assistance in the debugging the latest release. As always, we

Cancer Cancer

updated 22.2 years ago • A.J. Rossini

questions, e.g. just counting the number of transcription factors in a gene set by connecting to a public database? Many thanks, Rainer _________________________________________________ herausragenden Schutz gegen

Transcription GO convert Transcription GO convert

updated 15.8 years ago • Rainer Tischler

<div class="preformatted">Hi all, as many before, I have hard time in modeling a design matrix for a 24-slide cDNA experiment, including 4 experimental animals (each with 3 regions studied), 4 controls, and a dye swap! Thus, no common reference and no before/after data (I saw these kinds of matrices previously posted), and many possible levels of analysis (by animal, by region, or by experi…

updated 21.4 years ago • Giovanni Coppola

div class="preformatted">Hi all, I am attempting to use public MAGEML data without success. My current datasets are E-CAGE-{2,3,4} from ArrayExpress. According to the tutorial a MAGEML

ArrayExpress ArrayExpress

updated 22.2 years ago • Cary Miller

to the appropriate list -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington

Cancer Rgraphviz Cancer Rgraphviz

updated 16.8 years ago • rgentleman

would be very useful for my work. Thanks. -Colin -- Colin Alexander Smith cas277@nyu.edu PGP Public Key: http://certserver.pgp.com/pks/lookup?op=get&search=0xD604005F</div

Annotation affy Annotation affy

updated 23.6 years ago • Colin A. Smith

if you have any question. Cheers, H. -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109

Cancer Cancer

updated 15.3 years ago • Hervé Pagès

ami-85d88de0" (bioc-3.2-starcluster-ubuntu-14.04-100GB-201510141230) of type "m3.medium" gets me a public URL that works just fine for accessing RStudio server. But when I append \`:4200\` to that same URL, I consistently get a "Problem

ami

updated 10.0 years ago • joshmobrien

by a combination of gene expression and epigenetic profiling techniques and integrates either public or custom information of TAD boundaries.` What I am missing is a statement on its application on non-cohort data. We have

InTAD

updated 6.5 years ago • ATpoint

8 v1.1 (ILMN_xxxx). Thanks, Chao-Jen -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M1-B514 PO Box 19024 Seattle, WA 98109

Cancer Cancer

updated 14.5 years ago • Chao-Jen Wong

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

maanova maanova

updated 22.0 years ago • Lang Chen

<div class="preformatted">Dear List, I have been searching the Internet for CEL files for the Golub (1999) AML and ALL CEL files. I am interested mostly in the training data (38 files - 27 ALL and 11 AML). Are they publically available? Second, if they are not, and all we have is the golubEsets package, how were these data normalized & summarized...CEL files. I am interested mo…

updated 19.2 years ago • McGee, Monnie

and share it with the research community. -Update the description of your tool (availability, publication, programming language, etc.). Feel free to contact me if you have any questions or issues. -- Sent via the guest posting

Microarray Microarray

updated 12.1 years ago • Guest User

as issue and the vignette's oral squamous cell carcinoma dataset doesn't make any clinical details public. Is using only a set of widely accepted housekeeping genes a better approach that a set of the most variable ones

edgeR Exploratory Data Analysis

updated 8.8 years ago • Dario Strbenac

I tried to visualize the PCA plot after batch effect was modeled following this [post][2], using: log(counts(dds, normalized=TRUE) + 1) - log(t( t(assays(dds)[["mu"]]) / sizeFactors(dds) ) + 1) ![enter image description here][3] I thought some hidden

deseq2

updated 6.7 years ago • C T

If it is less than 0 it is a negative fold change # Need to make it positive, take the anti-log and then make it negative again # Else just calculate the anti-log if (log.fold.change < 0 ) { x <- -1 * log.fold.change fold.change

Cancer Cancer

updated 22.6 years ago • Claire Wilson

Hi all, I've been following the "RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR" vignette for usign limma on miRNA-seq data. I've gotten to the point of comparing the mean-variances pre- and post-filtering my data based on CPM counts. I'm a bit bugged by the differences in x-axis labels between the plot generated by voom() and plotSA() and I'm trying to understand if they ar…

limma

updated 6.7 years ago • AS

read the documentation, parameter maxExon > ecs <- fitDispersionFunction(ecs) Error in if (sum(log(coefs/oldcoefs)^2) < 0.005) break : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In glmgam.fit(mm...disps[good], start = coefs) : Too much damping - convergence tolerance not achievable 2: In log(coefs/oldcoefs) : NaNs produced > head( fData…

updated 11.6 years ago • Guest User

correspond to testing the interaction dataChip::conditionKd. Does this make sense or does it violate some of the assumptions? Does this not correspond to measuring the fold change of Input vs WT ( FCiwt ) and the fold change

edgeR deseq2 chipseq limma

updated 8.5 years ago • k.vitting.seerup

the corresponding dye-swap. Aims: ------ My motivation is to see if using amplified RNA alters the log ratios in comparison to total RNA. I am following a paper by Nygaard et al 2003 entitled "Obtaining reliable information...2002(3). In this paper they performed two investigations: a) Multiple hypothesis testing of log ratios to identify those genes whose log ratios were significantly differen…

limma limma

updated 19.5 years ago • Andrew Mcdonagh

src/R/getBinExpr.R) into the function told me that medianFIDist is assuming the data has been log transformed. This assumption is false. All my FCS parameters are still linear. I did not perform a transformation on them...r/base/stop.html">stop</a>('NULL control frame -- no control tubes specified?') #Note: assumes log transform has been applied, so relinearises before subtracting …

flowbin

updated 8.2 years ago • kelly.joanne.andrews

Dear Bioconductor Scientists, I am rather new to NGS data analysis, I learned what I know all by myself as there is no bioinformaticians where I work. Nevertheless, I already analyzed my own affymetrix HTA 2.0 data, as well as a couple public data on affymetrix HGU133 and Illumina HumanHT12 V3/4 microarrays (and should analyze some Agilent 4x44K soon). In the...where I work. Nevertheless, I al…

meta-analysis

updated 8.7 years ago • giroudpaul

who have strong background in statistics and programming (e.g. PhD in statistics with relevant publications) are also welcome to apply and will be given special consideration, even though they do not have much experience...the German TVöD (Bund/Ost) scale(E13) ### Application Please submit your application (CV including publications, two reference contact details, degree certificates (diplomas)…

rnaseq snp chipseq Job

updated 9.6 years ago • altuna akalin

the output of high-throughput runs for quality and biological meaning ? Contributing to the publication of results ? Developing and publishing new analytical methods, where needed ? Contributing to the CCD?s software...Curriculum vitae listing education, qualifications, and experiences, including a list of scientific publications The information in this e-mail is intended only …

Sequencing Microarray Cancer Sequencing Microarray Cancer

updated 13.4 years ago • Wittner, Ben

of Biostatistics and Computational Biology at Dana-Farber Cancer Institute/Harvard School of Public Health. The goal of the Yuan Lab is to develop computational approaches to analyze and integrate genomic data with...interpretation, and integration of genomic data-types is required. Lead author in at least one publication in major peer-reviewed scientific journals. __Additional Information:__ …

cancer computational biology rnaseq chipseq Job

updated 11.2 years ago • gcyuan

specialists on cross-functional teams, and the broader research community through presentations and publications. Requirements ============ * A PhD in a relevant field, including — but not limited to — Computational Biology, Bioinformatics...Proven track record of analyzing high throughput genomics data as evidenced by high quality publications and/or conference talks in this area. * Understan…

Transcriptomics SingleCell JobPosting

updated 5.0 years ago • Steve Lianoglou

a volcano plot using DESeq2 for a single-cell study transformed into pseudobulk. I am applying log fold change shrinkage using the apeglm method. However, the resulting plot looks unusual. It does not resemble a typical

DESeq2

updated 15 months ago • picasa1983

I was trying to identify the genes that are the most different between WT and KI mice based on log 2 fold change. I'm wondering why for some of them it shows NA for p value and p.adj value? ```r dds <- DESeq(ddsHTSeq_filtered...I was trying to identify the genes that are the most different between WT and KI mice based on log 2 fold change. I'm wondering why for some of them it shows NA…

DESeq2

updated 4.5 years ago • Yihan

exprs(affybatch)); > it gives different output......?? or should I do RMA which converts log base 2 values and then take antilog but..its still confusing..!! > do RMA(affybatch) > MatrixRMA <- exprs(myRMA); > MeanRawIntensities

affy affy

updated 21.0 years ago • SAURIN

hi, i am normalizing my CEL files with mas5 but i had negative values then i did like below befor log transformation but library(affy) Data<-ReadAffy() eset<-mas5(Data) norm.data <- sweep(exprs(eset), abs(min(exprs(eset))) + 5...hi, i am normalizing my CEL files with mas5 but i had negative values then i did like below befor log transformation but library(affy) Data&a…

affy mas5

updated 9.9 years ago • Angel

only accepts non-negative integers. CQN can be coerced to be non-negative, but is still on the log scale and cannot be coerced into integers. So because DESeq2 only accepts un normalized non-negative integers, then how

deseq2 cqn

updated 6.1 years ago • nicholas.macknight

how many probes there is in one spot for one type of 60 nt sequence in length. For instance, log-ratio tends to be approximately equal to zero (yellow spot after scaning slide) when the same sequence from two different

microarray

updated 7.0 years ago • w.abram

analysis using DESeq2, however I would like to compare my results with baySeq and in addition get a log odds for each gene, for every pair-wise contrast My experiment design is as follows: I have one grouping variable (Site) and

bayseq

updated 9.3 years ago • adityabandla

with princomp is that the function seems to scale the data by default. Since I am dealing with log rations there is no reason to scale the data because it is on a comparable scale. Is there some way of doing PCA in R on microarray

Microarray Microarray

updated 21.2 years ago • Johan Lindberg

assumed that the maxScore is the product of the column-wise Maximum of the PWM (since it is not on log-scale). However it seems that for both 'log2probratio' and 'prob' PWMs the maxScore is always the sum of the column-wise maximum

biostrings pwm

updated 9.4 years ago • Stefanie Tauber

share.pho.to/4e1QT I am a bit skeptical about the nature of my volcano plot, showing quite high log odds and skewed. Have I, in the process of playing around with the code, committed a mistake somewhere? Saket </div

Microarray Proteomics Cancer PROcess Microarray Proteomics Cancer PROcess

updated 12.0 years ago • Saket Choudhary

by our Firewall, but we do not know why this happens. There are no error messages and no entries in log files. Example Package:gahgu133acdf Url: http://www.bioconductor.org/packages/release/data/annotation/html/gahg u133acdf.html

cdf cdf

updated 15.5 years ago • Arcor

<div class="preformatted">Hi, I would like to specify normalization based on certain negative control wells using the package cellHTS2. I am trying: xn<-normalizePlates(x,scale="multiplicative",log=FALSE,method="negativ es",varianceAdjust="none",negControls=c("B12","C01","C12","D01","D12", "E01","F01")) but get: Error in checkControls(y...wells using the package cellHTS2. I am tr…

Normalization cellHTS2 Normalization cellHTS2

updated 18.1 years ago • Steve Taylor

higher (statistically)? Computationally, I know that if offsets are not provided, default offsets of log(lib.size) is used in the glmFit() function. The code on the svn seems to have been modified quite recently so maybe this will...function above), could I do something like this? myOffset = -offst(dataOffset) + log(lib.size) > head(offst(dataOffset), n=3) s1 s2 …

Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq

updated 12.8 years ago • Ying W

cells <- ellipsoidGate(filterId=filterId, .gate=cov, mean=mean) gate } > 2) Plotting on a log scale > When plotting, I have the log values on the axes. However, is it > possible to either: > a) plot on logarithmic axes...with the appropriate log binning, o > b) change the axis labels to be a log scale (even though the > axes are…

GO GO

updated 14.9 years ago • Roger Leigh

http://www.biomart.org' respond?    creating ensembl mart Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and ending tag mismatch: hr line...line 4 and html Premature end of data in tag html line 2 Error: 1: Space required after the Public Identifier 2: SystemLiteral " or ' expected …

PSICQUIC

updated 8.6 years ago • josemilezana

Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit

rstudio

updated 4.3 years ago • Fiona

https://support.bioconductor.org/p/88223/>, where the Bioconductor 3.3 AMI snapshot was made public for copying. Would it be possible to do the same for ami-9fe2fee4 (Bioc 3.5)? Thank you, Neal &nbsp

aws bioconductor aws ami amazon

updated 8.2 years ago • neal

MEcyan) to the left hand side of my eigengene adjacency heatmap? I’ve seen this figure produced in publications. Is there an argument for the plotEigengeneNetworks function that I can use? Here is my script that produces

R WGCNA

updated 6.2 years ago • normingt

Best wishes Robert -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington

Cancer Cancer

updated 18.8 years ago • rgentleman

Hi,  Does anyone have experience with standard rna-seq analysis tools (edgeR, DESeq2, etc) to detect allele-specific expression? I have a count table in which each F1 hybrid (3 biological replicates) has separate counts for the paternal and maternal allele. I am considering implementing a paired design in edgeR to test for differential allele expression between the parental alleles. How…

edgeR deseq2 ase allele

updated 10.2 years ago • trianglescout

a CEL file from processed data. We have a user here who needs to deposit their data in GEO for publication, but they have lost their original CEL file as the experiments were done 8 years ago. So, I was wondering if any of

probe probe

updated 13.5 years ago • J. Greenbaum

The clinician has advised me that the results are not possible to explain in any biological sense - nor with any time effect. We started thinking that there could be plate effect (technical effect) in the sequencing platform

limma

updated 3.1 years ago • mahes.muniandy