Bioconductor Forum

gt;to find genes that are significantly changed with the following >property: > > sign(log(ON/WT)) == -sign(log(KO1/WT)) and -sign(log(KO2/WT)) > >would the following design and contrast matrix be correct > >type = is a factor

limma limma

updated 19.1 years ago • Gordon Smyth

Hello, I have a question about the cpm function from edgeR. When I use this function with log = T, I get different results from when I use it without followed by log2 transformation afterwards. What did I miss here? Edit...behind this? Why is that better than just adding 0.5 read count? <pre> > CPM <- cpm(DGE1, log = T, prior.count = 0.5, normalized.lib.sizes = F) &gt…

edger cpm

updated 7.8 years ago • b.nota

DESeq2.html#why-un-normalized-counts][1] But, I want to try normalizing raw count into RLE(Relative Log Expression). 2. What does default statistical method of DEseq()? nbinomialwaldtest? thank you for your help. ```r # setup condition...Counts, colData = coldata, design = ~condition) # Estimate size factors using Relative Log Expression method dds <- estimateSizeFactors(dd…

normalization deseq2 StatisticalMethod

updated 2.8 years ago • SH

gt; Corrected array 3 > Corrected array 4 > Corrected array 5 > Error in optim(par = c(beta, log(sigma), log(alpha)), fn = normexp.m2loglik, > : > initial value in 'vmmin' is not finite That's a pity. We had hoped we had made this

limma limma

updated 20.5 years ago • Gordon Smyth

if there is a significant outlier, that is > suspect. The input to the above function is the log ratios for a > single array arranged in chromosome and position order. Hi, Sean What is the base of the log ratios for input

Normalization Normalization

updated 17.2 years ago • Zhi-Qiang Ye

100% Finished preprocessing. Begin genotyping... Start computing log-ratios -- Processing segment 1 out of 9 -- Processing segment 2 out of 9 -- Processing segment 3 out of 9 -- Processing segment 4 out...7 out of 9 -- Processing segment 8 out of 9 -- Processing segment 9 out of 9 Done computing log-ratios Leaving out non-variant SNPs Start calculating prior means Done calculat…

software error

updated 6.6 years ago • chuanjiao6

4 control samples and 4 cKO samples. However my log2FC values are inverted compared to the original publication. I think the issue is with how I define the control group (#set factor level) as the plotted data is always appears...symbol, pCutoff = 1e-4, FCcutoff = 1) > sessionInfo( ) R version 4.2.2 (2022-10-31) Platform: x86_64-apple-darwin17.0 (64-bit) Running un…

DESeq2 Log2FC RNASeqData

updated 3.0 years ago • Iwan

I have also listed the error I get below: Here is the code I run: library(aroma.affymetrix) log <- Arguments$getVerbose(-4, timestamp=TRUE) dataSetName<- "Test" chipTypes <- c("Mapping250K_Nsp","Mapping250K_Sty") cdfs...AllelicCrosstalkCalibration(cs,model="CRMAv2"); print(acc); csAcc <- process(acc, verbose=log); bpn <- BasePositionNormalization(csA…

updated 15.5 years ago • Manisha Brahmachary

the 10X dataset from which this dataset was sourced? 2) Could you please provide a reference to a publication or other document that confirms who and how the labels were obtained? Thank you for your time, Javier

labels PBMC SingleCellMultiModal 10X

updated 9 months ago • javier.ruizramirez

Do you like analyzing ‘omics data and want to have a stable job not reliant on grants and publications? Come work for HPCBio, a core service group in the Carver Biotechnology Center at the University of Illinois

Metagenomics GenomicVariation Genomics RNASeq ChIPSeq

updated 3.5 years ago • Jenny Drnevich

I analysed the enrichment GO using 'enrichGO' for two datasets independently. As suggested in this publication (https://github.com/GuangchuangYu/enrichment4GTEx_clusterProfiler), I combined the two enrichment results

clusterProfiler

updated 2.4 years ago • Valéria

Hello! I am doing DESeq2 for the first time. A bit of background: I am downloading the already public data available from ENA browser. I have been able to successfully do Kallisto on the paired reads. The output of such

DESeq2 Kallisto

updated 23 months ago • Aaliya

Hi all, I am using the package clustree as I have columns that contain the cluster assignments from clustering t with values of k from k=1 to k=N. Clustree can draw the tree but it only gives on kind of figure (a tree with visible nodes at all levels not very nice for publication). Still this is supposed to be a ggplot object so I would like to change it into a more standard tree (dendogram). …

ggplot dendogram ggtreeExtra clustree ggtree

updated 2.8 years ago • christian.dina

a lot, Benilton -- Benilton Carvalho PhD Candidate Dept of Biostatistics Bloomberg School of Public Health Johns Hopkins University </div

GO GO

updated 18.1 years ago • Benilton Carvalho

to grasp for someone without a rigorous statistical background and the vignette and the original publication did not enlighten me very much. Does this really mean I cannot use vsn on a data set that contains log2 transformed

vsn vsn

updated 19.6 years ago • knaxerov@ix.urz.uni-heidelberg.de

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 20.2 years ago • rgentleman

fax: (617) 632-2444 | | Department of Biostatistics office: M1B28 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+</div

updated 23.8 years ago • rgentleman

Hi Team, In our Azure environment NSG outbound rules are not allowed to public websites from any Linux VM. We have allowed specific IP ranges to allow https://bioconductor.org website. Problem is

software error

updated 5.9 years ago • vkatakwar

CRAN: https://cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt) Installing package(s) 'flowFDA' Old packages: 'foreign', 'nnet' Update all/some/none? [a/s/n]: a trying URL 'https://cran.rstudio.com

RStudio flowFDA

updated 3.3 years ago • kinoshamoodley

help me out, I would greatly appreciate it. **My data format** - Data for 11 years (2012-2022, with no data for 2013 ). - Data seasonally (4x/year for 11 years), but some years missing some seasons - Replicates vary per season

rain

updated 22 months ago • mpuli011

__res.data <- selectHKs(data, method = "geNorm", Symbols = featureNames(data), minNrHK = 2, log = FALSE) Error in R\[i\] <- Symbols\[ind\] : replacement has length__  any suggestions why I am getting this error thanks Shaun

normqpcr selecthkgs normalization

updated 7.9 years ago • s.m.may

x$table) <- value : attempt to set an attribute on NULL' after running logCPM.fit <- cpm(fit, log=TRUE). How can I fix this error? Is there a step that wasn't included in the example? Thanks

edgeR TimeCourse RNASeq

updated 4.8 years ago • hakusen03

where i have performed various filtering and normalisation steps using LIMMA. I now have a matrix of log ratios and was wondering which are people's preferred functions or tools to call genes as present or absent? thanks for

CGH limma CGH limma

updated 16.0 years ago • adam_pgsql

analysis? As I understand it the package calculates confidence intervals around the effect sizes (log fold changes). How do you analyse the results? Such as confect score threshold? Thanks, Jon [1]: https://bioconductor.org/packages

topconfects

updated 5.7 years ago • Jon Bråte

and-auc-and-ic50-of-a-dose-response-curve> regrading computation of AUC and IC50 from a log-logistic curve fitted to dose response data using PharmacoGx, I thought it would be helpful to share this with Bioconductor

dose-response PharmacoGx drc AUC IC50

updated 9.2 years ago • rubi

preformatted">Dear Friends, I want to know, is there in possibility to get M- values instead of log fold change value (logFC) in tapTable command used in LIMMA package? In case "yes", Please let me know how to do it? Thanking you

limma limma

updated 17.0 years ago • Prashantha Hebbar Kiradi [MU-MLSC]

Lecturers of the course: Robert Gentleman, Head of Program in Computational Biology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle (WA), USA. Wolfgang Huber, European Bioinformatics...England (UK). Rafael A. Irizarry, Department of Biostatistics, Johns Hopkins University, School of Public Health, Baltimore (MD), USA. The course is organized by S.M.Iacus an…

Microarray Proteomics Normalization Preprocessing Cancer Microarray Proteomics Cancer

updated 21.1 years ago • stefano iacus

Pathview is an open source software package distributed under GNU General Public License version 3 (GPLv3). Details of GPLv3 is available at http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users...are required to formally cite the original Pathview paper (not just mention it) in publications or products. For details, do citation("pathview") within R.   The pathview download…

gage kegg

updated 7.9 years ago • colaneri

coordinate) * Renamed "ENCODE region" filter to "ENCODE Pilot Regions", added a link to the publication (http://www.genome.gov/26525202)  *  Renamed the following Uniprot filters and attributes * "UniProt/Swissprot...80 * Renamed "ENCODE region" filter to "ENCODE Pilot Regions", added a link to the publication (http://www.genome.gov…

biomart Ensembl zebrafish Rat 1000 genomes phase 3 News

updated 10.6 years ago • Thomas Maurel

Hello, I am a Bioinformatics Research Assistant tasked with re-constructing our local sequencing centers analysis pipeline of RNA-Seq Data. I am following several tutorials for an RNA-Seq pipeline using EdgeR and Limma. I have 6 samples - 3 mock and 3 infected - and I have already had the sequencing center perform analysis and they saw that one of our infected samples seemed to be an outlier. …

Log2 edgeR RNA limma Normalization

updated 3.1 years ago • Sara

The result is showed in MAplot: ![enter image description here][1] I noticed some peaks with 0 log fold change are differentially biding sites, while it could be a little bit confusing. I see this result should be caused...sites without considering the overall gaining of signal? I can manually set a cutoff (e.g. abs(log FC) > 1) to determine, however the p-value and FDR should be re-ca…

DiffBind

updated 2.7 years ago • Ti

s function "aggTax" to aggregate:</span>     AggObj = aggTax(MRcounts(obj, norm=TRUE, log=FALSE),norm=TRUE, log=FALSE, lvl = Class, out = "MRexperiment") As you can see, I am using the normalized counts for aggregation, as

metagenomeSeq microbiome

updated 10.9 years ago • noelle.noyes

suspiciously?) large number of differentially expressed genes with adjusted p-values > 0.05 and log-fold-change > 1 (~3000). Also, the top log-fold change values are also very high (10-14). If I import the data and just log2 transform

neqc limma microarray illumina

updated 9.9 years ago • alexvpickering

array 8 Corrected array 9 Corrected array 10 Corrected array 11 Warning message: NaNs produced in: log(x) It seems that it stills gets zero value. Why would log(x) appears at this stage? I then normalize to see the print-tip loess

Normalization Normalization

updated 19.0 years ago • Yolande Tra

well known in cancer but this inconsistent result confuse me. Below is the picture. The x axis is log fold change reported by limma/voom and y axis is the log fold change reported by DESeq2. Each data point represent a gene

deseq2 limma voom limma-voom rnaseq

updated 7.1 years ago • bharata1803

come from and why there are so many differences? There a strong difference using un-transformed or log transformed values for dose, and since the control dose is 0.0mM which value to add for the log transformation. Are any rules

Regression DOSE Regression DOSE

updated 21.0 years ago • Arne.Muller@aventis.com

values being used for fold change calculation are not vst transformed. Also, being divided by log(2). ``` alleffects <- rbind(alleffectsBM, alleffectsSM) alleffectsVst <- vst(exp(alleffects), object) alleffects <- alleffects...log(2) alleffects <- alleffects - alleffects[, denoCol] ###foldChange ``` The calculation in the older version makes more sense for

DEXSeq log2foldchange Tutorial

updated 5.8 years ago • tmvarsha

15 Corrected 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) The datails of the medthod "normexp" is normexp = { for (j in 1:ncol(RG$R)) { x <- RG$G[, j

Microarray limma Microarray limma

updated 18.9 years ago • De-Jian ZHAO

gt; > > R CMD check "~/projets/ZeaMays/ZmB73_5b_masked/BSgenome_1.27.1.tar.gz" > * using log directory > '/projets/gear/scastelletti/ZeaMays/ZmB73_5b_masked/BSgenome.Rcheck' > * using R version 2.15.2 (2012-10...advance for the reply, > > Sara -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cance…

Cancer BSgenome BSgenome Cancer BSgenome BSgenome

updated 13.0 years ago • Hervé Pagès

specialists on cross-functional teams, and the broader research community through presentations and publications. - Identifying opportunities for public-private partnerships, e.g. by representing Denali within consortia...Experience in the field of neurodegeneration is a plus. - Experience accessing and managing public human datasets, e.g. PPMI, ADNI, UK Biobank or similar, is a plus. - Extens…

Biobase biomarker neuroscience biotech

updated 5.1 years ago • sandmann.t

I have cohort RNA sequencing data and clinical traits. Is the given code below fine to normalize and correct for Batch effect. For further analysis can we subject the processed matrix to WGCNA directly? data <- cpm(data, log=TRUE) design.Covariates <- model.matrix(~Batch) logCPM.adjusted <- removeBatchEffect(data, group=NULL, covariates=design.Covariates...For furth…

RNASeqPower removeBatchEffect cpm Batcheffect

updated 15 months ago • sukeshinik5

I don't have access to the raw counts. I am getting the opposite results as expected when using log(TPM+1) as a reference. Thanks! ```r # include your problematic code here with any corresponding output # please also include the

SingleR

updated 3.2 years ago • mea2712

data, I am using plotSA to check if there is a generally monotonic relation between the average log expression and the residual standard deviation. The plot detects a few outlier probes and highlights them in red. I was

limma

updated 3.6 years ago • S

confusion about the data preprocessing.  I downloaded normalized data and process it using log function. Then, the problem is coming, I want to ask whether can I process the data using Z-score function after the previous

limma camera

updated 8.3 years ago • django_w

gseGO is a gene list called "geneList". In this gene list, for each gene, there is a corresponding log fold change. But how can we calculate the correlation between each gene and phenotype if the input is just one single number

DOSE clusterprofiler

updated 8.4 years ago • xr2120

MCAR/MNAR) on two different groups within same dataset. Should I perform the imputation on raw or log transformed peptide intensity data? Kamal   &nbsp

msnbase

updated 8.5 years ago • kamal.fartiyal84

that have passed through marrayNorm ? & include normal ratio/intensity data rather than the log transformed options. *.Gf & *.Rf normalised data (similar to the output from VSN) thanks J.</div

updated 22.8 years ago • Jason Skelton

div class="preformatted">Hi I'm looking for a normalisation procedure which will normalise log ratio based on row only. I know the marray package has 2D normalisation, but I fired that at my data and it didn't touch it - the

marray marray

updated 18.1 years ago • michael watson IAH-C

community? Nominate for the New Contributions to Bioconductor Award! Nominations are open to the public and the deadline is May 31, 2023. Please fill out this [Nomination Form](https://forms.gle/gPzmH8ewHNHWckdv6) and be sure

Bioconductor Recognition Bioc2023 Awards

updated 2.7 years ago • shepherl

DE-Seq2 requires normalized counts. Suppose you have a public dataset where only normalized count data, for example TPM, is available. In that case would it be at all correct to probe

DESeq2

updated 4.6 years ago • Justin

the range of 0-1? I would be grateful if you could shed some light on this and/or direct me to any publications or webpages. Best, David </div

updated 17.5 years ago • darteta001@ikasle.ehu.es

in red... or change it to blue. I would like to make the output plots better to include in a publication out.groups <- see.genes(get.groups$sig.genes$mutantvscontrol, color.mode = "gray", newX11 = FALSE, k = 6, cex = 6, cex.xaxis

maSigPro graph

updated 5.1 years ago • Itzel

Hi there, I tried to re-analyse RNA-seq data that was made available on GEO and referred to in a publication. However, the only "raw" data that was made available was the rlog table extracted from assay(rld) (at least that's...Hi there, I tried to re-analyse RNA-seq data that was made available on GEO and referred to in a publication. However, the only "raw" data that was made available was t…

deseq2 rlog deseq

updated 8.1 years ago • sreibe

data and calculates tissue specificity. I am planning to make an R-package from this and go for publication. Before I begin packaging and writing drafts, I am doing my literature review and also looking to see if someone

tissue specificity r package package development

updated 7.9 years ago • YaGalbi

GenBank. NetAffx gives the same identifier for that probeset, but in a field called "Representative Public ID". There are some more probesets with "HGXXX-HTXXX" as ACCNUM on the hgu95av2 chip. Where can get more information about

Annotation Annotation

updated 18.4 years ago • Hans-Ulrich Klein

there is any different pattern of methylation between the regions in a tumour. So in this case I duo nor have any replicate I have one library for regionA and one library for region B in a tumour. I see you have some suggestions

RRBSdata

updated 23 months ago • annasoudi

in directory, which represent one batch. So, I am not specifying any parameters neither in R nor in FJ and using them by default. However, seems the flow rate check is more sensitive for outliers in FJ. It detects almost

flowAI

updated 22 months ago • Olena

Hi, I would like to try out ggtree as it appears to be very flexible. However, after the install via Bioconductor, I can neither load the sample trees nor any other trees. Install was on Ubuntu 16.04 and there were no errors. Any idea what is going on? I have no clues about R and I...be very flexible. However, after the install via Bioconductor, I can neither load the sample trees nor any other …

ggtree

updated 7.7 years ago • martin

RNAseq2_Gene_Norm = TRUE or Mutation = TRUE ``) works very well. Neither `` fileSizeLimit `` nor the project date are an issue here - I tried several. One thing I noticed in the <span style="background-color:Yellow">getFirehoseData

RTCGAToolbox

updated 8.8 years ago • federico.comoglio

gt; (this is as of Fri Sep 16 09:17:53 UTC 2011) > > I cannot resolve this domain from Holland, nor from California. Problem has disappeared; can reach the site now from both Holland California. Philip -- Philip Lijnzaad

Cancer PING Cancer PING

updated 14.3 years ago • Philip Lijnzaad