Bioconductor Forum

data in R. I used the following code to draw a loess fit and got the output as >?lines(lowess(log(abs(t(res))), log(abs(t(synthesised)))), col="red") Error in lowess(log(abs(t(res))), log(abs(t(synthesised)))) :?? NA/NaN/Inf in foreign function call...then used the commands which generated the error as follows -- > system.time(fit <- loessFit( log(abs(t(res))), log(abs(t(sy…

limma limma

updated 17.6 years ago • shetumi@aim.com

my Affymetrix GeneChip analysis by gcRMA. The file does not seem to exist neither on the repository, nor the bioconductor.org website. But the original affymetrix probe sequence file itself was available from affymetrix

xenopuslaevis probe gcrma xenopuslaevis probe gcrma

updated 15.9 years ago • Naoki Irie

and only the metadata, I'd rather not introduce a dependency on the huge BSgenome raw data packages nor on the BSgenome package itself, which has many dependencies; instead, is there a more streamlined way to easily get \*just

bsgenome chromosome reference genome

updated 7.9 years ago • Nathan Sheffield

sep=",") In my cvs file I get the name of genes, but I don t get the "F.p.value" nor "lods" values. I try: todos20050401.fit3$genes[selected,],todos20050401.fit3$F.p.value,todos 20050401.fit3$lods Error

updated 20.7 years ago • Marcelo Luiz de Laia

Hi all, I specifically have @drisso in mind for this question, but anyone who can help me is welcome. I've been thinking about this particular line from the RUVseq paper: "Properly behaved spike-ins could be a valuable resource for normalization: by design, their read counts are expected to be constant (or to have known fold-changes) between samples and hence any deviations from nominal fold-c…

RUVSeq RUVnormalize

updated 18 months ago • Erdi

3, hence the library sizes for day 3 is much smaller compared to day 5 - so my dataset are clearly violating assumptions of DESeq2. I would appreciate any tips/ideas you could provide - many thanks in advance! Miyako ```r # example

DESeq2

updated 4.6 years ago • miyakokodama

test(thus makes the assumption for equal variances between the groups of interest) could i have violated my results regarding the false positive rate ? Or due to the paired nature of my analysis(and thus not generally two

limma statistical inference variance test bioconductor

updated 10.6 years ago • svlachavas

significant they will have very low fold changes and thus be of questionable meaning) that we aren't violating the statistical underpinnings of the analysis. I need some help in justifying this filtering step. Does anyone

updated 18.8 years ago • Mark W Kimpel

install.packages("BiocManager") Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt) > > BiocManager::install("flowUtils") Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31 ucrt...libs\x64\xfun.dll: Permission denied #session information sessionInfo( ) R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) …

Bioconductor flowUtils

updated 3.1 years ago • Zoya

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070611/ 9ea99b69/attachment.pl

updated 18.6 years ago • arne.mueller@novartis.com

_ensembl") \`\`\`     but I get the following error: \`\`\` 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 …

biomaRt

updated 10.1 years ago • rmporsch

guid, gains, nodeInd, recompute, : ellipsoidGate::transforming can’t find transformation for FL 4 Log Loading the workspace seems to work fine and all samples can be loaded via the flowCore package with no issues. Is there...Creating ncdfFlowSet... All FCS files have the same following channels: Pulse Width FS Log SS Log FL 1 Log FL 2 Log FL 3 Log FL 4 Log FL 5 Log FL 6 Log TIME R…

flowWorkspace

updated 6.3 years ago • jokup101

r # Method 1: PCA based on LCPM y <- readDGE(files, columns = c(1, 3)) lcpm <- cpm(y, log = TRUE) dat <- t(lcpm) pca_res <- prcomp(dat, scale. = TRUE) autoplot(pca_res, data = dat_org, colour = 'group') # Method 2: VST dds <- DESeqDataSetFromMatrix

PCAtools edgeR pcaExplorer RNASeq RNAseq123

updated 3.7 years ago • Alan

status [1] "" $major [1] "4" $minor [1] "2.0" $year [1] "2022" $month [1] "04" $day [1] "22" $`svn rev` [1] "82229" $language [1] "R" $version.string [1] "R version 4.2.0 (2022-04-22)" $nickname [1] "Vigorous Calisthenics

R-4 ShortRead

updated 3.2 years ago • Bogdan

recommend a workaround? Maybe the server is having a bad day but it is hard to tell. Here is a log of what is happening: > ids=c("GO:0009058","GO:0015995") > pngamigo=getAmigoTree(goIDs=ids,color="pink",filename="test_bp.png...picType="png",saveResult=T) Error in readPNG(aa) : unable to open <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> <html><head> <t…

RamiGO RamiGO

updated 11.8 years ago • suzy.stiegelmeyer@syngenta.com

Hello, I am new to R and flowCore but have been able to figure out most elements of the package that I need.  However I need to apply a hyperlog transform to a number of parameters in my flowFrame and I can't seem to figure out how that is done correctly. Currently I am applying a standard log transform in the following way:   f <- read.FCS('MyFile.fcs', tra…

flowcore flow cytometry flowdensity hyperlog transformation

updated 7.4 years ago • Joseph.Hanson

CRAN: https://rweb.crmda.ku.edu/cran Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10) Warning message: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'AnnotationDbi

AnniotationDbi

updated 3.8 years ago • Kelly

to get involved in organizing BioC2022, planned to be in a hybrid format in Seattle July 27-29, 2022. There is lots to be done, including sponsorship and funding, outreach, website, workshop technical organization, program

bioc2022 Conference

updated 4.1 years ago • Levi Waldron

getURL(" http://bioconductor.org/packages/2.3/bioc/bin/windows/contrib/2.8/ABar ray_1.10.0.zip ") nor : getURL(" http://bioconductor.org/packages/2.3/bioc/bin/windows/contrib/2.8/ABar ray_1.10.0.zip ",file="target.zip") P.S. How

updated 17.2 years ago • li lilingdu

it in the report. Thanks, Hajar BLData=readIllumina(arrayNames=array.namen,backgroundMethod="none",nor malizeMethod="Quantile",useImages=F) 'useImages=FALSE': please check that the 'singleChannel' argument is appropriate for

updated 14.7 years ago • Hajar Hassani Lahsinoui

some direction or some material that addresses such problem. I am considering "system()" but I am nor sure how far can I go with this. Help appreciated. Thanks -- Fahim Mohammad CECS, univ of Louisville [[alternative HTML version

Alignment PROcess Alignment PROcess

updated 15.7 years ago • Fahim Md

coverage to annotated ORF-based coverage, if the genome of interest is NOT supported in neither UCSC nor ENSEMBL, which means that creation of a TranscriptDB object in a straightforward way (I.e. according to the GenomicFeatures

Coverage Annotation TranscriptDb convert GenomicFeatures Coverage Annotation TranscriptDb

updated 15.2 years ago • Oleg Moskvin

class="preformatted">Hi all, Can someone tell me where I can find xtable package? Neither biocLite() nor getBioC() works for me since our company's computer does not allow the connection. I usually download the packages manually

updated 20.2 years ago • Li,Qinghong,ST.LOUIS,Molecular Biology

Hi there, I would like to clarify some concepts about DESeq normalization: 1)How does DESeq account for RNA compostion in the "median of ratios" method (if so, in which step of the code/formula)? 2)Kind of stats question, why is the geometric mean more appropiate than arithmetic mean for the pseudo-sample created to obtain the size factors? 3)How reliable is DESeq on ~10 samples per condit…

deseq2 rnaseq normalization

updated 7.8 years ago • xavi

it in the report. Thanks, Hajar BLData=readIllumina(arrayNames=array.namen,backgroundMethod="none",nor malizeMethod="Quantile",useImages=F) 'useImages=FALSE': please check that the 'singleChannel' argument is appropriate for

updated 15.2 years ago • Hajar Hassani Lahsinoui

We have a bacterial mock community consisting of 22 bacterial taxa. The mock community exists in 2 basic versions - one in which each taxon is (supposed to be) equally abundant, and one in which one of the species has inflated abundance (at several different levels).  We would like to use the mock community datasets to test our wet lab and bioinformatics pipeline. Our idea was to constr…

edger deseq2

updated 10.3 years ago • Nick N

span style="line-height:1.6">> ensembl = useMart("ensembl")</span> Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Opening and ending tag mismatch: hr line...body line 4 and html Premature end of data in tag html line 2 Error: 1: Space required after the Public Identifier 2: SystemLiteral " or ' expecte…

biomaRt

updated 10.2 years ago • Cheng-Yuan Kao

from Diffbind table back to expression values (basically unlog it). My question is whether the log used to calculate the log fold change is log or log2? I looked at the DiffBind manual and it says "The Fold column shows the...log fold changes(LFCs) between the two groups, as calculated by the DESeq2 analysis." I am assuming it is done using log2 transformation

DiffBind

updated 2.6 years ago • bhandary.8590

0.999999437256152 -4.75598562188099 So AveExpr = Amean But I have looked at the 'average log-intensity' for the raw values and for the fitted coefficients for log10, log2 and log and looked at mean(log(x)) and log(mean...I can post the data if need be. Moreover, many of the fitted coefficients are less than zero and log(mean(x)) is defined but not mean(log(x)). Can anyone tell me how Amean (a…

updated 15.1 years ago • Michael Muratet

https://mirror.las.iastate.edu/CRAN Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10) Warning message: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'biomaRt

biomaRt

updated 3.8 years ago • Kelly

The complete sequence of a human genome" by Nurk S, Koren S, Rhie A, Rautiainen M, et al. Science, 2022. A SNPlocs data package for dbSNP Human Build 155 (1 billion SNPs): https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP155.GRCh38

BSgenome dbSNP T2T-CHM13v2.0 SNPlocs

updated 3.7 years ago • Hervé Pagès

I have started a public Mendeley group to track and share publications related to bioconductor packages.  Consider adding the citation

bioconductor publication News

updated 9.3 years ago • Sean Davis

differentially methylated CpGs/regions? The beta and M values have bimodal distributions which violates the normality assumption, I wasn't sure if another transformation was needed in order to achieve a normal distribution

minfiDataEPIC minfi

updated 2.4 years ago • phelankj

open="r")) ## Error: Error in h5checktypeOrOpenLoc(). Argument neither of class H5IdComponent nor a character. ``` Is there a way to provide a connection to `rhdf5` methods instead of having to expand the zipped file on disk

rhdf5

updated 3.0 years ago • merv

of me, as I am a part of you. That's American. Sometimes perhaps you don't want to be a part of me. Nor do I often want to be a part of you. But we are, that's true! I guess you learn from me--- although you're older---and white--- and somewhat

GO GO

updated 22.8 years ago • Eric

can also be extracted out of illumina tif-files (if for whatever reason the annotation file is nor available). Thanks for any help. Cheers /Christian/ </div

Annotation Annotation

updated 17.8 years ago • Christian Kohler

<div class="preformatted">Hi all, I'm picking up on an older thread (https://stat.ethz.ch/pipermail/bioconductor/2006-August/013881.html ) which poses the following question: What are the most appropriate methods for normalization in the face of large numbers of differentially expressed genes? Aside from this 2006 thread, I've found only one publication on the topic (http://www.ncbi.…

Normalization limma Normalization limma

updated 16.5 years ago • David Garfield

CRAN: https://cran.rstudio.com/ Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31) Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TRUE` to re-install...CRAN: https://cran.rstudio.com/ Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31) Installing package(s) 'ChIPseeker' trying URL 'https://bioconduct…

Bioconductor BioCManager ChIPseeker

updated 3.0 years ago • ASIF

here below my concern during Biobase package installation; ``` if (!require("BiocManager", quietly = TRUE)) + install.packages("BiocManager") > > BiocManager::install("Biobase", force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.…

GSVA Biobase

updated 2.8 years ago • johann.brisseau

Hi, Normalized counts from the matrix table are transformed to log2 values by metagenomeseq, aren´t they? My question is about the zeros in the count matrix. How are they transformed to allow statistical analysis? (as log2 of zero gives an error). Thanks!

metagenomeseq logtransformation

updated 9.0 years ago • PJ

Hi, I am trying to plot(matplot) values vs log2 concentrations values which I know that some of you do all the time. On the x-axis instead of the log2(x) values, I would like to replace the axis values with the original x values as boxplot does. Can someone tell me a trick so that I would be able to put these original x-values on the x-axis? Thanks, Lana [[alternative HTML version delet…

updated 20.9 years ago • Lana Schaffer

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070111/ 42636922/attachment.pl

updated 19.0 years ago • Mohammad Esad-Djou

How do I calculate the error associated with aggregated L2FC values? I'd like to combine multiple differential expression values into a single statistic, with variance, to express how genes in the mitochondrial complexes change (or don't change) compared to wildtype cell lines under certain conditions. Here's an example of a graph I'd like to reduce to a simpler line-with-error plot (possibly …

deseq2

updated 6.5 years ago • David Eccles (gringer)

I can install CRAN packages. getOption("repos") is correct. but not Bioconductor packages, nor BiocManager. > config <- "https://bioconductor.org/config.yaml" > readLines(config) Erreur dans file(con, "r") : impossible

Install

updated 7 months ago • delphine

some data in R using the Gviz package, but I can't seem to get the gene names to appear on the track nor can I get the ideogram function to work. For the ideogram, I am aware that the yeast genome does not have cytobands, but I would

gviz Saccharomyces_cerevisiae Gviz ideogram

updated 2.3 years ago • Michael

allows you to plot PC1, PC2, and PC3 against each other but does not provide the actual numbers, nor does it provide access to any further PC's. Any help with this would be greatly appreciated. dba.PCA documentation: https

DiffBind dba.plotPCA

updated 4.7 years ago • Spendlove

package, but Affy refused and recommended I use the oligo or xps package.  But neither oligo nor xps install in R 3.1.1 so I downgraded to R 2.15.2. Now I can install oligo, but it asks for the annotation package - pd.hugene.2.0.st

affy oligo

updated 9.9 years ago • WATSON Mick

can be used to analyze continuous data sets. My experimental design does not include any "treatments" nor "replicates". Its simply a gene expression counts along an environmental gradient (with more than 200 samples, spanning

edger

updated 6.4 years ago • avihai.zolti

2. Gene expression correlation ( all to all)__ Since I got R 3.3.3 run on R-studio, neither Biobase nor limma is compatible. It is greatly appreciated that if someone can help me with detailed scripts.  _R > install.packages

R differential gene expression

updated 8.7 years ago • lvu2

On our cluster I have installed R to a staged location that other users share for use, but I remain the user that manages the staged installed binaries. The cluster doesn't share the user's home location (they share a mounted path where the data is placed). We want to know if we are able to have the users specify where their bioconductor installs go so they don't have to ask for my help every tim…

installation

updated 11.1 years ago • goochmi

to nominate](https://forms.gle/u7iWAiRUYaB8pR4H8) someone. The deadline for nominations is May 20, 2022

Bioc2022 Awards Bioconductor Recognition

updated 3.8 years ago • shepherl

font like Courier.] The linear model says that for each gene, the Expected Value of the "observed" log-ratios vector is equal to the design matrix multipled by the vector of log-ratio(s) (parameters) to be estimated. Sometimes...estimating the log-ratio(s) of interest is simply a matter of averaging the "observed" log-ratios from the raw data. (But it's also nice to estimate...ApoAI KO data se…

zebrafish limma zebrafish limma

updated 22.5 years ago • James Wettenhall

lrtFreqCutoff function (p0, p1, n = if (C == 1L) 1L else n, C = 1L) { num <- (1/n) * log(C) + log(1 - p0) - log(1 - p1) denom <- log(p1) - log(p0) + log(1 - p0) - log(1 - p1) num/denom } > VariantTools:::BinomialLRFilter function (p.lower = 0.2

VariantTools VariantTools

updated 12.1 years ago • heyi xiao

saying - "I think you are referring to a 24 fold increment in numbers aren’t you or is the start log 0.1? If for example they start at log 2.0, or 100 cfu/g, then a 24 fold increment would take it to log 48. It may be more useful to...identify where you are going to and from where – eg log 1 to log 6 – as this is more interpretable". OUT baseMean = 17.61369762 log2FoldChange = 24.21197847 …

deseq2

updated 6.8 years ago • tegan.sutton

n.cores.max = 1, outputDir = ".", overwrite = T) ``` log gives a Warning, that apparently the extended Sequence is not right: ```r Loading required package: BiocGenerics Loading...I doing something wrong? **UPDATE** Actually, it does not matter the values set in baseBeforegRNA nor baseAfterPAM flags, e.g. setting them both as '1' yields the same result as th…

CRISPRseek

updated 3.6 years ago • Miguel

I would like some help getting DE genes from what is turning out to be a more difficult design than I thought. The data come from elsewhere, so the design isn't mine (nor can I just repeat everything). I want to get DE genes from different times in fetal mouse development (E14 and E16), so comparing 2 different gestational ages. I also want to look at fetal sex as a variable. My proposed analysis…

edgeR RNAseq voom variability estimator

updated 5.8 years ago • hcnbox

I'm trying to extract a certain entry from annotationhub, but I keep getting a "Public" error.  Any idea how to fix this? library(AnnotationHub) hub <- AnnotationHub() org.PA01.eg.db <- hub\[\["AH48516"\]\] Error...in hub\[\["AH48516"\]\] : Public I am able to extract other entries e.g. "AH4

annotationhub

updated 8.7 years ago • ecpierce

calcNormFactors(data, method = "upperquartile") #All normalization methods with log data lcpm_none = cpm(cpm_none, log=TRUE) lcpm_TMM = cpm(cpm_TMM, log=TRUE) lcpm_TMMwsp = cpm(cpm_TMMwsp, log=TRUE) lcpm_RLE = cpm...cpm_RLE, log=TRUE) lcpm_upperquartile = cpm(cpm_upperquartile, log=TRUE) #box plots normalized #NONE png('box_plot_none.png') boxplot...TMMwsp', ylab= 'Log-cpm' ) de…

RNAseq123 Rna

updated 3.6 years ago • Mikołaj Mierzejewski

has been moved from TCGA data portal to [Genomic Data Commons](https://gdc.cancer.gov/about-data/publications/skcm_2015). I spent some time and found this [link](https://tcga-data.nci.nih.gov/docs/publications/skcm_2015...DCC\]:[unc.edu\_SKCM.IlluminaHiSeq\_RNASeqV2.Level\_3 \[tar.gz\]](https://tcga-data.nci.nih.gov/docs/publications/skcm_2015/unc.edu_SKCM.IlluminaHiSeq_RNASeqV2.Level_3.1.10.0.ta…

concatenated TCGA files RNASeq matrix

updated 8.1 years ago • yifangt

see which BioMart databases are available > list<-listMarts() 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 …

biomart

updated 10.2 years ago • s.corley