Bioconductor Forum

My answer was that the "change" was not necessarily surprising. For example , when you have "true log signal" from a bimodal distribution logS=c(rnorm(1000,3,1),rnorm(1000,8,2)) # You will see this has two peaks par(mfrow=c(2,2)) plot(density...logS)) #if the background, log(non-specific binding) come from logB=rnorm(2000,6,1) #then when you plot the histogram of convolution...in log scale, plot…

Normalization probe Normalization probe

updated 19.6 years ago • noel0925@sbcglobal.net

data, to compare the expression profiles between 2 conditions. I get different results when using log-expression values to when I'm using (z-score) normalised log-expression values. Do you know why that could be, how scaling could...affect a t-test? Should I use the scaled or unscaled log-expression data? Thank you so much for your help

limma

updated 6.6 years ago • Regeroka

2.2.0 and 2.2.5  both GDCPrepare() return a function. \`\`\` function (x, df1, df2, ncp, log = FALSE) <pre> { if (missing(ncp)) .Call(C_df, x, df1, df2, log) else .Call(C_dnf, x, df1, df2, ncp, log) }</pre

TCGAbiolinks

updated 9.2 years ago • jvwong

Error in .var_OR_get_meta_or_gene(var, object) : pred21@meta.data is not a metadata or gene nor equal in length to ncol('object')" ```dittoBarPlot( object = JHMV21, var = "pred21@meta.data") # and this is the singleR part ```JHMV21_counts

RNASeq ditto dittoSeq SingleR

updated 24 months ago • Fayrouz

www.biomart.org and verify if this website is available. Error: XML content does not seem to be XML, nor to identify a file name Can somebody suggest me, how to get out of this error? Regards, mlsc [[alternative HTML version deleted

biomaRt biomaRt

updated 13.8 years ago • MLSC MANIPAL

immediately. You should not retain, copy or use this e-mail or any attachments for any purpose, nor disclose all or any part of the contents to any other person."* [[alternative HTML version deleted]] </div

updated 11.7 years ago • Abugri James

the commen reference have the same distribution. But with dye swap, I can not use neither "Rquantile" nor "Gquantile". What should I do? Or other normalization suggestions? Regards, Yanju Zhang </div

Microarray Microarray

updated 18.7 years ago • yanju@liacs.nl

Hi, due to a strange error in DESeq my group is finally being forced to switch to DESeq2 (probably a good thing). There is one problem we are not sure how to solve, though: In the old DESeq, we would normalise the data and then call nbinomTest() for each comparison we wanted to make. Now, the DESeq() function does all in one, which is nice up until you don't want to compare everything …

deseq2 deseq

updated 8.6 years ago • LilithElina

would be a quite common task but I did not find any function that would do this. Neither scanBam nor readBamGappedAlignments are directly helpful with this. For me the most obvious thing would be to hold the alignment

Alignment Alignment

updated 14.2 years ago • Hubert Rehrauer

CRAN: https://cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt) Installing package(s) 'microbiome' trying URL 'https://bioconductor.org/packages/3.15/bioc/bin/windows/contrib...CRAN: https://cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt) Installing package(s) 'phyloseq' …

GenomeInfoDbData microbiome phyloseq

updated 3.4 years ago • kikiki

<div class="preformatted">Hi Joyce, > 1, I use read.marrayRaw() to read into my data into R, and found I have a lot > of NA value, I would like to know what is the algorithm to calcualte this > value. It is log ratio, do you also have certain kind of thresh value to cut > off? read.marrayRaw doesn't do any thresholding or cutoff. The...lot > of NA value…

updated 21.9 years ago • Jean Yee Hwa Yang

CRAN: https://cran.rstudio.com/ Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.1 (2022-06-23 ucrt) Installation paths not writeable, unable to update packages path: C:/Program Files/R/R-4.2.1/library packages

ALL

updated 3.5 years ago • xxxsarahkimxxx

<div class="preformatted">Dear all, I am trying to package up some microarray data analysis code into a bioconductor package and, naturally, I want to define some new generic functions using the methods library. I have not been able to get my package to pass rcmd check. In particular, generic functions which I have defined are not recognized when rcmd check tries out the examples. Howeve…

Microarray Microarray

updated 22.9 years ago • Gordon Smyth

dispersions. Maybe replicates have not been properly specified.") Would changing the code this way violate any assumptions of the DEXSeq model? Thank you, Mani PS: # condition + batch terms are redundant as sample term is already

safe DEXSeq safe DEXSeq

updated 12.6 years ago • Narayanan, Manikandan NIH/NIAID [E]

features, and I'm not sure what the best offset would be (I use 0.5). I did notice that the log-cpm values output by each method are a bit different (see below). The first plot uses the log-cpm from voom, and the second uses...log-cpm from the cpm() function with prior.count = 0.5: ## log-cpm from voom: ## ![voom log-cpm density plot][2] ## log-cpm from cpm(log = TRUE, prior.count...0…

limma limma-trend voom RNASeq

updated 4.1 years ago • Tyler Sagendorf

1.6">cts <- txi$counts</span> normMat <- txi$length normMat <- normMat/exp(rowMeans(log(normMat))) library(edgeR) o <- log(calcNormFactors(cts/normMat)) + log(colSums(cts/normMat)) y <- DGEList(cts) y$offset <- t(t(log(normMat

tximport edger salmon rna-seq

updated 9.2 years ago • Peter

<div class="preformatted"> Dear All, I hope it is OK to send a general request for images to the bioconductor mailing list. Nature journal is about to publish a Feature on the statistical analysis of DNA microarray experiments. The Bioconductor Project is mentioned in the article. I am looking for pictures to illustrate the text and am hoping that you might be able to provide me with ima…

Microarray Microarray

updated 22.5 years ago • Loriot, Sarah

I am looking at making mCG calls at single CpG sites, and have been looking at methylPipe for this reason.  I have a query about the functioning of BSprepare. When BSprepare loads up the \#C/\#T values at a locus, if coverage<50 at a particular nucleotide, then it seems that it looks up the p-value of the site being methylated from a lookup table, which has been populated from bi…

methylation methylPipe

updated 8.2 years ago • jonathan.moore

package="KEGGgraph") g <- parseKGML2Graph(colFile) Error: does not seem to be XML, nor to identify a file name as you can see I got warning message, is it ok? I don't think it worked properly, since I got error after

KEGGgraph KEGGgraph

updated 15.1 years ago • Yan Jiao

I wonder how DEseq2 is calculating the fold change and p-value !? There is neither any warning nor any error ! should I slice the data 3 different combination of each group ?! The second question I have is about `` condition

deseq2 phyloseq time course

updated 9.3 years ago • akp

for DGE. However, i cant seem to find the correct annotation file with the IDs and gene symbols, nor can I find this specific platform on biomaRt. Any help would be greatly appreciated. Thank You ``` > gse <- getGEO("GSE37147

Annotation biomaRt GEOquery

updated 3 days ago • Manav

M and A - as my reference (Cy3) remains pretty much constant, then as Cy5 increases, so do both M (log(ratio)) and A(average log(intensity)) (this can be demonstrated by plotting M vs log(Cy5) and M vs log(Cy3) - the positive correlation

updated 21.3 years ago • michael watson IAH-C

div class="preformatted"> [1]NatWest logo Introducing Text Alert System. Log In into your account and update your mobile phone number. [2]Click here to Log In Please do not reply to this email address...as it is not monitored and we will be unable to respond. For assistance, log in to your HSBC account and choose the "Help" link on any page. ^HSBC BANK P.L.C Refe…

updated 16.1 years ago • HSBC

<div class="preformatted">So here goes, I am about to risk getting myself blacklisted by the very people I can least afford to be blacklisted by, and at the very start of my career no less. Why am I taking this risk? Because I love Bioconductor, it's the most useful thing currently installed on my PC, and I'm deeply grateful to the developer and user community for making such a wonderful to…

GUI GUI

updated 21.9 years ago • Alex F. Bokov

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...times before it eventually fails. Also, it does not always fail at the same row of the dataframe, nor is there anything obviously wrong with the data value…

updated 15.0 years ago • Elliot Joel Bernstein

pre> mart = useMart(biomart = 'unimart',dataset='uniprot',verbose = T) 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 ' expected 3: SYSTEM or …

biomart uniprot unimart

updated 10.1 years ago • john

I am trying to create a VariantExperiment object from a VCF, but I am getting this error: ```r Error in validObject(.Object) : invalid class “DelayedAperm” object: only dimensions equal to 1 can be dropped ``` The GDS object is created successfully, so the problem is happening in `makeVariantExperimentFromGDS`. I see that I am failing a validity check, but not sure where. Any suggestions w…

VariantExperiment

updated 3.4 years ago • chase.mateusiak

glm functionality. Essentially I want to find genes where (keeping the paired structure intact) log(Drugged_TN/Drugged_T0) << log(Undrugged_TN/Undrugged_T0) or log(Drugged_TN/Drugged_T0) >> log(Undrugged_TN/Undrugged_T0

RNASeq RNASeq

updated 13.1 years ago • Simon Knott

  We work on the legume Chickpea which genome has been recently released but it does not have a BSgenome package so far. I though I'd try and make...nbsp; We work on the legume Chickpea which genome has been recently released but it does not have a BSgenome package so far. I though I'd try and

bsgenome bsgenome forge

updated 8.5 years ago • jodiera

<div class="preformatted">Hi, This has been asked a few times but I'm unable to find an answer. When you run >esetgcrma2 <- gcrma(data, fast=FALSE) #OR esetgcrma2 <- justGCRMA(fast=FALSE) #You get this error Adjusting for optical effect......Done. Adjusting for non-specific binding.Error in bg.adjust.fullmodel(pms[, i], mms[, i], pm.affinities, mm.affinities, : …

gcrma gcrma

updated 21.2 years ago • Matthew Hannah

with summarization disabled (a summary argument has to be provided or it returns an error).  Nor can I use the function pm() because the probe to probeset id numbers are lost.  That is, with pm() the row identifiers turn

u133a normalization rma affy

updated 9.0 years ago • jxd_84

anybody know how I can get in touch ith the author of GOSemSim (Guangchuang Yu)? The package page nor the package contain an email address. Specially, my question regards the GO annotations of genes that come with the package

GO GO

updated 16.6 years ago • Rajarshi Guha

one. The arrays I work with tend to have duplicates on each slide. However, they are not adjacent nor equally spaced and so when setting the spacing of the duplicates in limmaGUI (which appears to be compulsory) I just make

limmaGUI limmaGUI

updated 22.2 years ago • Peter Baker CMIS, Indooroopilly

div class="preformatted">Dear BioC people Could it be that neither detection.p.value (simpleaffy) nor mas5calls (affy) work with Hu6800 chips? I get the following errors: > M17 <- ReadAffy(filenames=c("M17.cel")) > dpv17 <- detection.p.val

hu6800 probe hu6800 probe

updated 20.8 years ago • Christian.Stratowa@vie.boehringer-ingel…

lt;- useMart(biomart = "ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org" ) #Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Entity 'nbsp' not defined Error: 1: Space required...after the Public Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing 4: Entity 'nbsp' not defined #[repeat 5 times

software error biomart ensembl

updated 9.5 years ago • genomicsio

limerick/bioconductor-community-manager-22064][1]. Note the application closing date is 7th June 2022 (11am GMT). Please share this opportunity via your networks - thank you! [1]: https://www.universityvacancies.com/university

Community Teaching Bioconductor

updated 3.6 years ago • Matthew Ritchie

I have a matrix with TPM values called 'expr' and a list of gene sets 'list'. The TPM matrix is not log-transformed but rather directly derived from the salmon output via tximport. This is my code: <pre> TPM <- tximport(files...experiments or some other kind of continuous value derived from __RNA-seq__ counts such as log-CPMs, log-RPKMs or log-TPMs. This flag should be set __to __…

gsva rnaseq tpm

updated 8.3 years ago • leiendeckerlu

and Amean. However, AveExpr is not same as value of the fitted coefficients. AveExpr is the average log intensity for a particular probe across microarrays. The fitted coefficients will be the same as logFC value from the...topTable output. The coefficients are named as logFC in topTable output as the change in log intensities when treatment changes from 1 to 2 is equal to the value of coefficie…

probe probe

updated 15.1 years ago • Sunny Srivastava

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

Annotation Organism easyRNASeq Annotation Organism easyRNASeq

updated 12.9 years ago • Bayles, Darrell

on raw gene counts. Now for the future purpose, I want to combine replicates and calculate the log fold change values between control and experimental condition (I don't want to perform differential expression analysis...VST counts? I tried combining them by mean() which is basically geometric mean as the values are in log. But I noticed that log fold change distribution is drastically shifted (f…

DESeq2

updated 3.0 years ago • Jayesh Kumar

in Limma Is not correct. We input the expression values as log2 transformed values. The Average log expression value is then calculated by averaging the log values (ave(logX)). However, this is NOT the log of the average expression

updated 15.0 years ago • Lana Schaffer

edgeR) <pre> cts <- txi$counts normMat <- txi$length normMat <- normMat/exp(rowMeans(log(normMat))) library(edgeR) o <- log(calcNormFactors(cts/normMat)) + log(colSums(cts/normMat)) y <- DGEList(cts) y$offset <- t(t(log(normMat

edgeR TXIMPORT

updated 7.8 years ago • burcu.atasu

<div class="preformatted">Hi, I am running R 1.7.1 and a version of affy that I downloaded two days ago. I have been working through the examples in Chapter 4 from "The Analysis of Gene Expression Data". First, I noticed that image display using the log scale as described at the bottom of p. 104 will only work for me if I change R> image(CEL1, transfo=log()) to R> image(CEL1…

affy affy

updated 22.5 years ago • Chris Paulse

ALL) (found at MBI Lab4 by Sandrine Dudoit et al.) consists of 128 samples. But I read in the publication that 33 patients were evaluated by gene expression profiling. (Btw: the source http://bioconductor.org/Docs/Papers...gives only 30 CEL- files.. ?) Which of the 128 samples in ALL are the 33 mentioned patients in the publication? Moreover, it would be great to have the original R code behind …

updated 20.7 years ago • Heike Pospisil

data. Its functionality will be useful for my current project. I have not been able to find any publications validating or using this package. If anyone is aware of any relevant publications, I would be very grateful if

updated 10.8 years ago • Mirza, Nasir

nbsp;Could someone please tell me how the normalised counts N are calculated? See the formula below. log E\[Y |W, X, O\] = W α + Xβ + O.  Are the normalised counts simply log(Y)-Wα-O? If so, how can I get α from the output of RUVg? Also, log

RUVg ruvseq rnaseq

updated 9.5 years ago • Pauly Lin

list all available marts: <pre> > library(biomaRt) > listMarts() 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 ' expected 3:…

biomart bug

updated 9.7 years ago • Johannes Rainer

showWarnings = FALSE, recursive = TRUE) ah = AnnotationHub(cache = kCacheDir) # snapshotDate(): 2022-04-21 ah[kResource] # AnnotationHub with 1 record # snapshotDate(): 2022-04-21 # names(): AH100643 # $dataprovider: Ensembl # $species...Homo sapiens # $rdataclass: EnsDb # $rdatadateadded: 2022-04-21 # $title: Ensembl 106 EnsDb for Homo sapiens # $description: Gene and protein annotations for H…

AnnotationHub org.Hs.eg.db ensembldb

updated 3.4 years ago • sandmann.t

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...gt; > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > F…

Annotation GO Cancer Apis mellifera BSgenome Biostrings BSgenome rtracklayer goseq GO

updated 13.9 years ago • Alicia Oshlack

_mice\_vs\_log"   "genomeyb1.conditionmice" I need the following comparison: 1. mice vs log in all the samples 2. mice vs log only in v252 samples 3. mice vs log only in yb1 samples The way I defined the contrast for each...comparison: 1. contrast = c("condition","mice","log") 2. contrast = list("condition\_mice\_vs\_log") 3. contrast = list(c("condition\_mice\_vs\_log",…

deseq2 deseq rna-seq

updated 11.0 years ago • solgakar@bi.technion.ac.il

assessed. Do you thing I can use DESeq2 for differential expression in this assay? People in this publication used DESeq2 for assay https://www.htgmolecular.com/assets/htg/publications/2018_Myers_MicroRNA_Biomarkers_for_Parkinsons.pdf

Targetedsequencing DESeq2

updated 5.0 years ago • Fereshteh

data. I have found the file "EBPlusPlusAdjustPANCAN_IlluminaHiSeq_RNASeqV2.geneExp.tsv" from their publication website https://gdc.cancer.gov/about-data/publications/PanCan-CellOfOrigin . I understand that this was done

cancer limma deseq2

updated 6.3 years ago • KCLiv

output the respective values in the result-tab don't fit the plotted values in the "splicing" tab nor the "expression" tab. Are those the exon usage values and their fold change? Why are the numbers different from the heights

DEXSeq differential exon usage exon usage

updated 10.1 years ago • biominer

dropped. Once that happens then we no longer have complete sub-grids; normlizeWithinArrays will nor longer work with the printtip loess option. So I wish to make a modification to the normalizeWithinArrays function that

Normalization limma Normalization limma

updated 21.5 years ago • Peter Wilkinson

Thanks, Michael. That was the tip I was looking for. For what it's worth, neither args (ranges) nor ?ranges led me to the answer you so quickly provided. I spent more than a little time looking. I am a little timid about this

updated 16.6 years ago • Paul Shannon

numerical matrix of fake scatter and marker readouts. Thus, the data are not read with read.FCS nor saved as a flowFrame. Instead I save the matrix as a data frame (call it Ab). The data, generated by me, have all entries present

updated 16.8 years ago • Saumyadipta Pyne

for DGE. However, i cant seem to find the correct annotation file with the IDs and gene symbols, nor can I find this specific platform on biomaRt. Any help would be greatly appreciated. Thank You ```> > gse <- getGEO("GSE37147

Annotation biomaRt GEOquery

updated 3 days ago • Manav

Is the variable  Deseq$LRTStatistic equal to -2 Log(Likelihood of full model)  -  -2 Log(Likelihood of reduced model)  ??   Thanks

deseq2

updated 8.1 years ago • kulotwewe

replies. The issues are 1. Producing NAs during background correction 2. Quantile normalization on log or raw scale 3. Differential expression analysis (linear modelling) on log or raw scale Let's consider these in turn: 1. You...There exist no clear results on whether it is best to carry out quantile normalization on the raw or log scale. The function normalizeBetweenArrays() in the limma pac…

Normalization limma PROcess Normalization limma PROcess

updated 20.8 years ago • Gordon Smyth

I'm trying to understand how the mean-variance plot is calculated with the meanVarPlot() of EDASeq package. I tried to reproduce it manually with the code below but the result is very different. Given the expression matrix (row=genes, columns=samples), I used the logarithm to transform the counts before computing mean and variance. Since there are zero counts, I considered the  maximum …

edaseq

updated 9.6 years ago • neverstop