Bioconductor Forum

obvious/approaching it wrong. Thanks for your time and help! -Katie ``` R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Ventura 13.3.1

nullranges

updated 2.7 years ago • Kathleen

include the results of running the following in an R session sessionInfo( ) R version 4.2.2 (2022-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.2.1 Matrix products: default BLAS: /Library

read.FCS read.flowSet

updated 2.7 years ago • Pilid

I am working on a next generation sequencing data set from Human. I am wondering whether there is a public exon-exon junction library available. Thanks Shirley [[alternative HTML version deleted]] </div

Sequencing Sequencing

updated 16.4 years ago • shirley zhang

viewform) by June 15th. Nominations are open to the public

bioconductor bioc2020 award community News

updated 5.0 years ago • shepherl

that import packages not available at BioC or CRAN. The external package would be available at a public website instead. Assume that the licensing of the external package is appropriate. Thanks, Sam </div

updated 11.9 years ago • Samuel Younkin

Hello, Many publications use a combination of both padj and fold change ratio to define differentially expressed genes (DEGs) identified

deseq2

updated 5.4 years ago • marija.buljan.2

obtained from the definition of M and A. with the normalization rule: M'=M-Me_ij i.e. Normalized log ratio M' equals raw log ratio M minus the estimated log-ratio Me_ij from the M vs A plot of the two slides i and j. If we replace

Normalization Normalization

updated 21.2 years ago • Tarca Adi Laurentiu

Is it necessary to redownload packages every time I log off and re-enter R? If not how do I avoid this

phyloseq

updated 4.5 years ago • klltnq

transformation as follows : Baseline to median of all samples: For each probe the median of the log summarized values from all the samples is calculated and subtracted from each of the samples. In Cluster 3.0 It is recommended...to log transform the data and mean or median centre the genes to transform the data. What is the best way to go about base transforming

GO Clustering probe affy gcrma GeneSpring GO Clustering probe affy gcrma GeneSpring

updated 17.3 years ago • Ruppert Valentino

robust") fit2 <- contrasts.fit(fit,contrast.matrix) fit2 <- ebayes(fit2) I am ineterested in log fold change between the contrast samples, but the as I see it is not there my question is how can i get the log fold change between

updated 17.3 years ago • hemant ritturaj

sensitivity$chemosensitivity)Rx Sensitive" Now from limma output, I found genes with negative log fold change that are express higher in the insensitive samples and genes with positive log fold changes that are express

DEG Limma

updated 9.1 years ago • Shamim Sarhadi

y) I obtain different values if I calculate cpm in this way > cpm <- cpm(y, log = FALSE, normalized.lib.sizes=TRUE) Or in this one > cpm <- cpm(y$counts, log = FALSE, normalized.lib.sizes=TRUE) Why are them

edger cpm rnaseq

updated 5.4 years ago • francesca3

Corrected array 1 Corrected array 2 Corrected array 3 Corrected array 4 Error in optim(c(beta, log(sigma), log(alpha)), sumloglik, gr = grsumloglik, : non-finite value supplied by optim So I ignored the background and went ahead

Normalization Normalization

updated 20.6 years ago • Guoneng Zhong

Ontology http://current.geneontology.org/ontology/go- basic.obo With a date stamp from the source of: 2022-07-01 In the website for msigdbr v7.5.1 the data of the release is March 30th, 2022. https://www.rdocumentation.org/packages

org.Mm.eg.db GO msigdbr

updated 2.9 years ago • S

peer' ``` I went to KEGG and this notice was posted that KEGG API moving to HTTPS as of June 1, 2022: https://www.genome.jp/kegg/docs/announce.html . I think this may be the cause of my problem and also this recent post https...know what settings I need to change? Thanks, Jenny ```r sessionInfo( ) R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Runn…

limma KEGGREST EGSEA

updated 3.5 years ago • Jenny Drnevich

offst(dataOffset)) > > Then, I still believe that the cqn offsets should be multiplied by > -log(2) to be handed to edgeR, which is not currently in the cqn vignette: > > > design <- model.matrix(~ d.mont$sample$group) &gt...to provide an explicit formula for what is meant by "offset", > which could be one of: > > log(mu) …

GO edgeR cqn EDASeq GO edgeR cqn EDASeq

updated 12.8 years ago • Kasper Daniel Hansen

1] 128 Browse[1]> normalize function(x) x Browse[1]> p [1] 4 Browse[1]> param [1] "BL1.H Log" "BL3.H Log" "FSC.H Log" "SSC.H Log" Browse[1]> probBin [1] FALSE Browse[1]> saveFcs [1] FALSE Browse[1]> teller [1] 6 Browse[1]> p <- length

FlowCytometryData Phenoflow

updated 4.4 years ago • cy117

is that when you pass a matrix to lmFit(), it then has to try to guess whether the matrix contains log-ratios (from a two color array) or log-expression values (from a single channel array). It is better to pass the full object so...numeric|, |matrix|, |MAList|, |EList|, |marrayNorm|, > |ExpressionSet| or |PLMset| containing log-ratios or log-values of > expression for a series of …

Annotation probe limma Annotation probe limma

updated 12.8 years ago • Gordon Smyth

203.7 + 1 countToTpm <- function(counts, effLen) { rate <- log(counts) - log(effLen) denom <- log(sum(exp(rate))) exp(rate - denom + log(1e6)) } df$tpm <- with(df, countToTpm(counts, effLength)) With the

rnaseq counts tpm GenomicFeatures kallisto

updated 5.2 years ago • m93

specificity (or otherwise) of Presence calls from the MAS algorithm. Does anyone know of a publication in which this is discussed (intelligently). Stephen Henderson ********************************************************************** This email and any files transmitted with it are

updated 21.3 years ago • Stephen Henderson

can I specify the version (eg ENSEMBL 39 not 40) Thanks Aedin -- Aed?n Culhane Harvard School of Public Health, Dana-Farber Cancer Institute </div

Cancer biomaRt Cancer biomaRt

updated 19.4 years ago • Aedin Culhane

the ENCODE metadata. ``` > encode_df <- get_encode_df() snapshotDate(): 2019-10-29 Error: Public ``` Can someone help me fix that

annotation software error ENCODE

updated 6.2 years ago • zhiyue.zhao

PCA, I applied batch correction using the `removeBatchEffect` function from limma. Should I use this log-transformed, normalized, batch-corrected expression matrix as input for GSVA? Alternatively, is it possible to run GSVA...on the log-transformed normalized expression matrix before batch correction and then include the batch variable in the differential

GSVA GSVAdata RNAseq

updated 18 months ago • Lucy

you help me solve this problem? ![This is the example of table. X1 is the gene name and X2 is the Log fold change. There are much more genes in the table.][1] ```r #unlisting gene id and log fold change Control_entrez_unlist_gene

KEGGgraph KEGG

updated 19 months ago • Fara

and normalizing for two factors i got the expressed data with lof2FC, pval and padj. Then i did log-fold shrinkage using the apeglm package and im getting differentialy-expressed genes with significant p-values...overlapping at the center of it, something that does not happen when differential expression without log-fold shrinkage is done. Is there any statistical criteria for selecting …

deseq2

updated 7.1 years ago • sherajilir

technical replicates in Genome Studio and use Group\_Probe\_Profile as input to lumi and proceed to log-transformation and normalization with this table OR ii) load the Sample\_Probe\_Profile in lumi, proceed to log-transformation

illumina human ht-12 v4 technical replicates

updated 10.0 years ago • Eleni Christodoulou

<div class="preformatted">Hi, I am just doing a straightforward analysis of mouse affy data using affy,gcrma and limma It is a simple 2 group design with not much complication to it. So this is a minor problem that I have been scratching my head since the beggining of the week, and cannot figure out the answer, so hopefully someone can help me. After I read my data, normalize and analyze a…

Biobase affy Biobase affy

updated 15.4 years ago • Lucia Peixoto

cts <- txi.rsem$counts normMat <- txi.rsem$length normMat <- normMat/exp(rowMeans(log(normMat))) o <- log(calcNormFactors(cts/normMat)) + log(colSums(cts/normMat)) and at the last line i got an error  _Error in calcNormFactors.default

tximport rsem edger

updated 7.9 years ago • tim.ivanov.92

to the DGEList in a similar way assays can be added to a SummarizedExperiment. I calculated the log transformed cpm values of a DGEList and I would like to store them in the DGEList, so subsetting this object would subset...the log transformed cpm values too. here is my code: query <- GDCquery(project = "TCGA-BLCA", # project-code for Bladder Cancer data.cate…

edgeR summarizedexperiment dgelist

updated 7.7 years ago • aljoscha.leusmann

interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error

limma limma

updated 13.7 years ago • Paul, Cristina

and instead is finding the site-wide g++ even though it doesn't have access to that version of g++, nor even access to the directory structure that contains the site-wide g++ (g++ is installed as a module on this linux box, and I haven

densvis docker

updated 2.7 years ago • James W. MacDonald

in my case does not. Also, when I told about this to CRAN team, they told me "...neither ChIPseeker nor your package can be installed in `R-devel`", which seemed to me like the core of my problem. So, is there anything I could do about

ChIPseeker cinaR

updated 4.8 years ago • Onur Karakaslar

the exon usage value in the splicing plot, however these value are neither stored in the html report nor in the DEXSeqResults object, instead they are calculated during the plot process. So is there a way that could output the

dexseq

updated 5.2 years ago • ywu

s+Disease"homo+sapiens.xml', reason 'Invalid argument' Error: XML content does not seem to be XML, nor to identify a file name 'query"Crohn's+Disease"homo+sapiens.xml' I suspect that, because I am trying a multiple word keyword

updated 13.6 years ago • Guest User

is not a valid argument, and this can be checked also looking at the code) and neither "cores.ratio" nor anything like it is a valid argument.   - p.8 of the PDF shows a function called "as.bootstrap.scores". However, that function

tronco

updated 9.7 years ago • Ramon Diaz-Uriarte

in sequencing depth between projects? Could there anything else in the data or analysis that could violate any assumptions made by edgeR? Is there any known problems with the newest version of edgeR? > sessionInfo() R version

Sequencing RNASeq edgeR Sequencing RNASeq edgeR

updated 12.0 years ago • Blum, Charles

since DESEQ2 was utilized to perform the differential analysis, does this means the "regularized log transformation" "DESeq2"  was applied to the raw count value?  Or in my case above, simple log transformation of "TMM...here](https://support.bioconductor.org/p/95842/): so it seems to me that in my case, the "conc" is log transformed counts  normalized by library size.…

diffbind

updated 8.6 years ago • JunLVI

ChIP QC report: E2F7 and E2F8", reportFolder="ChIPQCreport") sessionInfo(): R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621) Matrix products: default locale

ChipQCReport

updated 3.1 years ago • stacy.genovese

Enter the body of text here When I try to execute the code in the 'recount quick start guide' (https://bioconductor.org/packages/release/bioc/vignettes/recount/inst/doc/recount-quickstart.html#1_Basics): ```r ## Load library library("recount") ## Find a project of interest project_info <- abstract_search("GSE32465") ## Download the gene-level RangedSummarizedExperiment data download_…

recount

updated 3.7 years ago • nathan-temple

of name "elementMetadata" for this object of class "RGChannelSet" sessionInfo( ) R version 4.2.2 (2022-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.3.1

ageData missMethyl differentialvariability minfi

updated 2.7 years ago • Saanchi

Ontology http://current.geneontology.org/ontology/go- basic.obo With a date stamp from the source of: 2022-07-01 ----- Thank you very much

GO.db

updated 2.7 years ago • RuBBiT0

with significant points on the plot being marked with motif PWMs, if anyone can point me to a publication or some interesting code it would be much appreciated. Thank you

pwm motifs jaspar meme motif analysis

updated 7.1 years ago • rbronste

L-BFGS-B need finite values of ‘fn’</em> <em>…</em> <em>Warning messages;</em> <em>1: In log(row.z.likelihoods[i, state]) : NaNs produced</em> <em>2: In log(row.z.likelihoods[i, state]) : NaNs produced</em> <em>3: In log(row.z.likelihoods...i, state]) : NaNs produced</em> <em>4: In log(row.z.likelihoods[i, state])…

clomial

updated 8.1 years ago • Jouni Kujala

df$W and df$NormalizedCounts. However, the normalized counts are in logCPM and I would like to back log them for data exploration purposes. This level of stats is a bit over my head (I'm a PhD physiology student) so I am struggling...to understand what direction to take my code to back log them. If I simply take the normalized counts and apply 10^(x+1) I get counts that seem unreasonably high.…

RUVSeq CPM Normalization

updated 3.6 years ago • Jess

xlim = c(-2,2), ylim = c(0,6), xlab = bquote(~Log[2] ~ "fold change"), ylab = bquote(~-Log[10] ~ italic(P)), axisLabSize = 12, title = paste("NanoString -",data.name), subtitle = '', labFace = "bold", pointSize

EnhancedVolcano

updated 3.5 years ago • junli1988

a problem for affy arrays or does it also affect spotted ones? Cheers, Amy. > -GCRMA assumes log normal distribution for background. It also assumes > that the parameters of that log normal distribution depends on

probe affy gcrma probe affy gcrma

updated 19.9 years ago • Amy Mikhail

However, when I use bioconductor to normalize the data (e.g., maNorm) I only end up with matrices of log ratios (maM). How do I compare the expression levels of the two groups if I only have the log ratios (and not the normalized expression

Microarray Normalization Microarray Normalization

updated 22.2 years ago • Robert Cribbie

not able to find the R command to obtain the list of Differentially expressed genes at a Fold change (log-fold change) and FDR cut-off. The R command __summary__: <pre> summary(de <- decideTestsDGE(et, p=0.05, adjust="BH"))</pre> only gives...of the top "n" number of DE genes. I am interested in getting the__ full list of DE genes at the log fold change cut-off of (+-1) and…

edger rnaseq

updated 11.2 years ago • candida.vaz

A figure here. So, let me try to explain the result from the figure. So, when looking at the figure (Log-fold change x Average log-Expression), I can see a few genes highlighted in green and red. These genes are between the range...of  -2<log-Fold change <2. My question is: If I got <span style="background-color:Yellow">0 up- and down-regulated genes</span> in …

Treat method Number of DE genes

updated 8.3 years ago • Sanches

gt; packageVersion("haven") [1] ‘2.5.1’ > R.version$version.string [1] "R version 4.2.2 (2022-10-31)" > BiocManager::version() [1] ‘3.16’ > sessionInfo() R version 4.2.2 (2022-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running

S4Vectors DataFrame haven_labelled haven

updated 3.1 years ago • Daniel E. Weeks

the email addresses of at least one referee as a single PDF document and no later than March 31st 2022 to info.proteomics@ls.tum.de. Online interviews will be conducted with selected candidates and remaining shortlisted...School and individual research groups. All successful candidates are required to start October 1st, 2022 link: https://www.baybioms.tum.de/open-positions/proteome-feed-the-wo…

JobPosting

updated 3.9 years ago • mengchen18

02-24 [1] CRAN (R 4.3.0) cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0) digest 0.6.31 2022-12-11 [1] CRAN (R 4.3.0) evaluate 0.20 2023-01-17 [1] CRAN (R 4.3.0) fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) htmltools 0.5.5 2023-03...04-28 [1] CRAN (R 4.3.0) rmarkdown 2.21 2023-03-26 [1] CRAN (R 4.3.0) rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.3.0…

limma

updated 2.6 years ago • sarah.kelliher

source filter * Renamed "ENCODE region" filter to "ENCODE Pilot Regions", added a link to the publication (http://www.genome.gov/26525202)  * Ensembl Variation 82 * Renamed filters and attributes from variation...dataset * Renamed "ENCODE region" filter to "ENCODE Pilot Regions", added a link to the publication (http://www.genom…

ensembl biomart News grch37 GRCh37

updated 10.3 years ago • amonida

in minifi both give me the same .convertArray_450k_epic error: ```r snapshotDate(): 2022-10-31 snapshotDate(): 2022-10-31 see ?FlowSorted.Blood.EPIC and browseVignettes('FlowSorted.Blood.EPIC') for documentation...annotation: 20a1.hg38 ``` Session Info: ```r sessionInfo( ) R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) …

FlowSorted.Blood.EPIC minifi

updated 22 months ago • Kim

We wish to analyse an Exon Array dataset we obtained from a public source (unfortunately not GEO). The data we have is a matrix of RMA normalised expression values from some 400 Exon arrays

normalization oligo limma

updated 10.5 years ago • i.sudbery

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updated 18.3 years ago • Li, Aiguo NIH/NCI

hi, I have a question regarding technical replicates of the same biological sample. I have for a sample the following: sample1-rep1 sample1-rep2 Sample2-rep1 Sample2-rep2 etc up to 12 The individual samples are biological replicates while the the sample (rep1 and 2) are technical replicates from the same tissue. My question is, for DESeq2, should th…

deseq2 normalization

updated 5.3 years ago • A

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updated 18.7 years ago • James Anderson

Hi! I am doing pairwise comparisons with DESeq2 (version 1.24.0). I would like to shrinkage the log2 Fold Change using the normal approach. I used the following code: dds <- DESeqDataSet(se_sel, ~ condition) dds <- DESeq(dds) resNorm <- lfcShrink(dds, contrast=c("condition", cond1 , cond2 ), type="normal") resNorm log2 fold change (MLE): condition cond1 …

deseq2

updated 5.7 years ago • dequattro.concetta

Dear all I am new to microarray analysis and have been assigned a rather challenging project. I'd like to re-analyze published microarray data from GEO. Essentially I would like to do a differential gene expression meta analysis, between diseased and healthy, across different experiments, chips and species (mouse, human). I more or less just started and found the bioconductor package GEOque…

GEOquery microarray lumi affy limma

updated 5.6 years ago • fabian