Bioconductor Forum

for 6 of the slides here: http://mcnach.com/MISC/scatterplots.gif these are Cy3 vs Cy5, in log scale. These show that many genes are differentially expressed, and they are mostly one one side only (upregulated; some...of those slides are dye swaps). Would this appear to violate (too much) any of the assumptions made by loess normalisation? Should I investigate other normalisation procedures

updated 19.4 years ago • J.delasHeras@ed.ac.uk

Bioconductor users, for your information, the Bioconductor Code of Conduct committee's response to a violation reported at BioC2019 has been posted at [`https://bioc2019.bioconductor.org/code_of_conduct`][1]. [1]: https://bioc2019.bioconductor.org

bioc2019 News

updated 5.8 years ago • Levi Waldron

one of my normals). I was told that I could > use a function like > >> log(eset/esetRef,2) > to generate the new matrix containing log ratios. Wow. That was some horrible advice. Please stop relying...First, please note that RMA normalized intensity values are already on the log_2 scale. So taking logs again isn't necessary, nor advisable. Second, why are you…

multtest limma siggenes convert multtest limma siggenes convert

updated 13.9 years ago • James W. MacDonald

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Asia BioCAsia Conferences Events BioC

updated 3.2 years ago • Peter Hickey

Pixologic ZBrush Key 2022][1] [1]: https://clickonmac.com/pixologic-zbrush-crack-serial-key-version

PixologicZBrushKey2022

updated 3.3 years ago • clickonmac

BioC Asia is returning December 1-2, 2022 and this year we'll be running a hybrid event! The in-person event will be held in Melbourne, Australia as a satellite event...submissions are now open: - Registration: [https://www.abacbs.org/registration#!event-register/2022/11/28/abacbs-2022](https://www.abacbs.org/registration#!event-register/2022/11/28/abacbs-2022) - Abstract submissions for...bioc…

Asia BioCAsia Conferences Events News

updated 3.2 years ago • Peter Hickey

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

Bioc2022 Awards Bioconductor Recognition

updated 3.8 years ago • shepherl

div class="preformatted">Hi, I was wondering if anyone knew of a publication that demonstrates how GCRMA is superior to RMA. So far I have only been able to find some powerpoints? Thanks so

updated 21.3 years ago • Margaret Gardiner-Garden

div class="preformatted">Can anyone direct me to some research publications which make use of both quantile normalization and RMA? Thanks -- ---------------------------------------------------------------------- Matthew Hobbs Garvan Institute of Medical Research

Normalization Normalization

updated 22.5 years ago • Matthew Hobbs

<div class="preformatted">Hello, It has come to my attention that there are a couple of Bioconductor mirrors out there that neither the Bioconductor nor the R teams are aware of. It is fine to mirror Bioconductor, but we encourage you to let us know if you do so. The advantages of...my attention that there are a couple of Bioconductor mirrors out there that neither the Bioconductor nor th…

updated 14.3 years ago • Dan Tenenbaum

now however is whether this pre-filtering, i.e. removing of low count features, interferes or violates the assumptions of the dispersion estimation (or any other assumption) in the DESeq2 model (Also considering that...comes from the (ancient) field of microarrays were a variance based pre-filtering was thought to violate assumptions of the moderated t-test in limma. Is the situation similar for…

deseq2 pre-filtering

updated 10.7 years ago • Johannes Rainer

class="preformatted">Hi, I probably have a stupid question, but how do I specify that my data is in log in siggenes? I know in the window version of SAM, one can check if the data is in log scale or not, what about in siggenes? is log

updated 20.8 years ago • Ashley Lin

class="preformatted">Hi all, can somebody give me website addresses where it is possible to download public free available Affymetrix U133A CEL files thanks for your help Philippe</div

updated 21.8 years ago • Phguardiol@aol.com

There is now a public google calendar to advertise Bioconductor related events, conference, meetings, forums, etc. It can be accessed at...There is now a public google calendar to advertise Bioconductor related events, conference, meetings, forums, etc. It can be accessed at: [Calendar

Bioconductor events News

updated 5.6 years ago • shepherl

How do I generate a simple table similar to the following link in R http://www.fedstats.gov/policy/publications/wp1fig1_text.html Table 1 Poverty status, by age, 2000 Does anyone know the exact commands? Apologizies for

updated 15.6 years ago • David Lyon

everyone has heard of it, it makes reviewers happy). So, it would be nice to be able to point to publications in good journals so that reviewers will be comfortable. (I personally, am quite comfortable with SAM). --Naomi At

Microarray Microarray

updated 21.5 years ago • Naomi Altman

I have some doubts on the Feature extraction output. In output, I find all intensity values (example: log ratio, rProcessedSignal, gProcessedSignal, gMeanSignal, rMeanSignal etc) are given in log base 10. Now my question is, 1. Whether...it is common to measure microarray binary data (TIFF) in log base 10 or log base 2? 2. In case, measuring microarray intensities in log base 10 is …

Microarray limma Microarray limma

updated 16.9 years ago • Prashantha Hebbar Kiradi [MU-MLSC]

I download the dataset using geoquery and would like to perform log-normalize the dataset I try the log2 way but I need to do log-normalize what should I modify my dataset wrong way: ```r eset.log...lt;- log(exprs(eset), 2) eset.log[1:5,1:5

codelink

updated 4.7 years ago • Yuxiii

they have learned to their own research problems. - More details: [https://bioconductor.github.io/2022-09-12-BiocIntro-Heidelberg/](https://bioconductor.github.io/2022-09-12-BiocIntro-Heidelberg/) - Registration: [https://forms.gle

Workshop

updated 3.5 years ago • Laurent Gatto

switched to processing cel files through rma and the raw data produced from this processing is log base 2. My lab has noticed that log transformation Is not very visible with high p.values (above 0.1), but spreads them all

updated 22.7 years ago • Park, Richard

div class="preformatted">I am trying to understand the details of the RMA algorithm in terms of log transform. The probe level data obtained from ReadAffy is obviously not log transformed, so in the 3 steps: 1. background...normalization: 3. median polish summarization. should the algorithm work on raw data (without log transform) or log transformed data for these steps? I was trying to judg…

Normalization probe Normalization probe

updated 12.9 years ago • Jack Luo

nbsp;makeTxDbFromBiomart also by reproducing the function help examples. 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 3: SYSTE…

software error maketxdbfrombiomart

updated 10.1 years ago • luigi.cerulo

Hello, I'm using edgeR (in the Trinity-RNA Seq Pipeline) to do a differential expression analysis and when I try to make a heatmap I got the following error: __> gene\_cor = NULL > gene\_dist = dist(data, method='euclidean') > if (nrow(data) <= 1) { message('Too few genes to generate heatmap'); quit(status=0); } > hc\_genes = hclust(gene\_dist, method…

edger differential gene expression

updated 8.9 years ago • cvergarapulgar

couldn't find it explicitly stated anywhere in the vignette, the original paper, the SCAN help page nor searching on the support site what scale the resulting normalized values are on. From their distribution, I'm assuming...it's a log scale, but since the range of values for my samples is only from -1.8 to 5.2, I assume it's not the standard log2? The equations...in the paper use log() in severa…

scan.upc

updated 10.4 years ago • Jenny Drnevich

The 2022 Ascona Workshop on “Biological systems: from first principles to data-driven modelling and back” will be held in Ascona...Switzerland, March 27 to April 1, 2022. It is currently planned in-person only. Contributed presentations are welcome. Confirmed invited speakers include

theory modeling statistics ascona Workshop

updated 4.2 years ago • Wolfgang Huber

I don't have any further information about the data how it's processed., the data is not normalized nor log transformed

DESeq2 DifferentialExpression

updated 16 months ago • Ibrahim

div class="preformatted">Hi I am writing as I am trying to analyse NGS data from public data (GEO) specifically datasets such as one sample per time point. The raw (somewhat processed data) is 3 samples at different...write at the moment to see if this analysis works and obviously when I come to more complicated public data with replicates I will have to invest some time in learning the bioc…

Transcription DEGseq Transcription DEGseq

updated 13.3 years ago • Jill Pleasance

it to an expression-set using GEOquery. However, even though the values are normalized, they are not log-transformed which is kind of bad, since I'm using limma to analyse the samples. Is it possible to log-transform the values...of an eSet directly (without using exprs()), or can I tell limma to log-transform the values while using fit() or topTable

expressionset bioconductor limma geoquery

updated 9.2 years ago • bi_Scholar

div class="preformatted">Hi, I'm using BioC to analyze Peptide Microarrays. I'm looking for some public datasets to deeply test my scripts. Does any of you know some places or links ? I know that this could be an inappropriate

updated 18.6 years ago • Davide Valentini

This tutorial describes the tools used to access public data from the NCBI Gene Expression Omnibus and the Sequence Read Archive. Tools covered include GEOquery, GEOmetadb

geoquery geometadb sradb Tutorial

updated 4.8 years ago • Sean Davis

Dear DESeq2 developer and colleagues, DESeq2 generates an output table including "log2FoldChange". I have two questions about this value. I. As far as I know, this is a moderated version, not a log2 fold change from the raw count value. But I want to have unmoderated value that can be calculated from count directly and my current way is: (1) get normalized count (2) log transformation (3) …

deseq2

updated 6.5 years ago • bioinfo

There seems to be a colon and a space missing from the citation. I think it should be: > Terry Therneau, Steven Hart and Jean-Pierre Kocher (2022). Calculating samples: Size estimates for RNA Seq studies. R package version 1.36.0. See below for the current output: ```r citation...the citation. I think it should be: > Terry Therneau, Steven Hart and Jea…

RNASeqPower citation

updated 3.5 years ago • stephenjjohnson

<div class="preformatted">Hi all, I am trying to convert RMA normalized intensity values in my matrix (generated from Affymetirx raw .CEL data composed of ~30 tumor samples and 7 normal samples) to log ratios in which the intensity values from each tumor sample are compared with a reference sample (in this case I chose one...generated from Affymetirx raw .CEL data composed of ~30 tumor sam…

convert convert

updated 13.9 years ago • Mark Baumeister

a performed a typical differential expression analysis using limma voom and I want to extract the log cpm values to draw ROC curves. But I want to extract the log cpm values produced specifically by limma because they are normalised

limma edgeR RNASeq

updated 20 months ago • Shaimaa Gamal

Hi, I understand that the presence of negative log-transformed count values is a common occurrence in RNA-seq data analysis and these values are not necessarily problematic...for statistical analyses. I used `TMM` method > log transformed and used limma for identifying significant gene expression (see below). Then, I extracted few genes for (line...increasing from +150 --> + 250), …

Visualization Normalization ggplot2 edgeR

updated 2.6 years ago • Sabiha

to bioconductor as a part of my PhD. I am aiming to get my package on bioconductor and then write a publication for it to a journal. This would mean I do not have a citation to add to the INST directory. Is it OK not to have a citation

package-creation citation submit-package

updated 6.0 years ago • k.patel5

pars_q) Tue Nov 8 13:43:17 2022: SizeFactor estimation ... Tue Nov 8 13:43:17 2022: Controlling for confounders ... Tue Nov 8 13:43:18 2022: Using the autoencoder...implementation for controlling. [1] "Tue Nov 8 13:43:26 2022: Initial PCA loss: 8.33004023797846" [1] "Tue Nov 8 13:44:47 2022: Iteration: 1 loss: 6.74682189972167" [1] "Tue Nov 8 14:01:36 2022: Iteration...2 l…

R OUTRIDER BiocParallel

updated 3.2 years ago • me.achleitner

I am currently working on a single-cell data analysis project, and I am facing a challenge regarding the aggregation of single-cell data into pseudobulks for input into the GSVA software. GSVA only accepts a gene X subject matrix, which means that pseudobulks must be created to facilitate this input. I have come across two different approaches to the aggregation process and I am unsure of which o…

pseudobulk scRNAseq GSVA

updated 2.7 years ago • Tadeoye

parts of the Reference Manual but I still have not stumbled across the answer. I know that the log(CPM) is taking into account the estimated dispersions and the library sizes so it a bit different from the CPM directly...the fold change? Which of the 2 results would you state in a table showing your RNAseq results in a publication? __________________________ Christian Schrøder Kaas PhD student…

RNASeq edgeR RNASeq edgeR

updated 12.4 years ago • CSRK (Christian Schrøder Kaas)

<div class="preformatted">Here is just a lil "trivia" statistic question for the forum:-) I apologize for my clumsy annotation but i hope I get the question through anyhow:-) For ratios I take it its normal procedure to calculate the average as the geometric mean. That is easiest done with log transformed values, giving something like <r> = mean(Ratio=a/b)=2^ (<log2(a)> - <…

Annotation GO Annotation GO

updated 19.1 years ago • Jesper Ryge

div class="preformatted"> Hi I am writing as I am trying to analyse NGS data from public data (GEO) specifically datasets such as one sample per time point. The raw (somewhat processed data) is 3 samples at different...write at the moment to see if this analysis works and obviously when I come to more complicated public data with replicates I will have to invest some time in learning the bio…

DEGseq DEGseq

updated 13.3 years ago • Guest User

Table(x) + mymatch <- match(probesets, tab$ID_REF) + return(tab$VALUE[mymatch]) + }))) Error in log(c("27", "59.8", "34.1", "110.5", "130.3", "569.3", "210.5", : Non-numeric argument to mathematical function Can u please help me solving this

GEOquery GEOquery

updated 17.3 years ago • hemant ritturaj

class="preformatted">Hi, I was unable to find a emthod/parameter to draw tickmarks corriesponding to LOG decades for flow-cytometry data. I have then implemented my method (is brutal but seems effective). RESULT: http://img510.imageshack.us...i/pkhlinear.png/ CODE: # SET number of channels and log decades channels <- 65535 decades <- 4 plot(mData[[1]], "PE", breaks=256, col=…

updated 14.9 years ago • drambald

TMM method in edger one gets lots of values <1. Unfortunately, I found neither in edger manual nor in edger paper the description how the log fold change is calculated. Especially how those values <1 are treated because

edger normalization logfc

updated 10.0 years ago • tonja.r

Hello, I'm running this code to get the fitted log-CPM values after running voomLmFit, but it doesn't work. ```r v <- voomLmFit(y, modsv, block = samples$clone, keep.EList = TRUE) cpm.fit.tab...works with DGEList. Looking at the output voomLmFit has EList. Does EList contain the fitted log-CPM values? If not, can you please recommend how to get the fitted log-CPM values from the o…

limma edgeR

updated 3 months ago • Lina

or other means. Have a good candidate (or multiple candidates)? Please nominate them by May 20, 2022. Applications are open to the public and any individual may submit more than one nomination. More information and details

Recognition Awards Bioc2022 Bioconductor

updated 3.7 years ago • shepherl

is a continuous variable (range 0-1). The analysis work out fine, and I am inclined to think the log scale is not essential. However I am not completely sure. My question therefore: Can the LIMMA package also be used for data...that is NOT on a log scale? Many Thanks, Marco MPM Boks, Rudolf Magnus Institute of Neuroscience, Department of Psychiatry B01.206, University

limma limma

updated 18.2 years ago • Boks, M.P.M.

div class="preformatted">The limma change log is no longer linked to from the URL http://bioinf.wehi.edu.au/limma but instead is distributed as part of the package itself

limma limma

updated 21.4 years ago • Gordon Smyth

different > bases. > > Also, at least in the usage with which I am familiar, "natural: logs > are > base e not base 10" and I have seen "log" without a subscript used for > both base 10 and base e logs. So even if B is not...if you look at the code in eBayes.R, you will see that the B-stat is computed with the R function 'log', and if you look at th…

limma limma

updated 19.7 years ago • Darlene Goldstein

Hi, I'm using DNAcopy to segment copy number log-ratios, and I was wondering if somebody here is aware of reasonably well-tested code that jointly uses b-allele frequencies...SNPs to achieve better results.  It would be fairly trivial for example to find optimal log-ratio segmentation parameters (alpha etc.) by minimizing the segmentation error of mirrored b-allele frequencies (1-frequ…

sequencing snp

updated 10.3 years ago • markus.riester

<div class="preformatted">Hello all, I'm analyzing a set of data that turns out to be a little unusual, but related to the recent discussions on what to do if you have a large (>40%) proportion of genes changing . I'd like some advice on my approach, particularly from the point of view of a manuscript reviewer... Here's the scenario: I get a set of 6 affymetrix chips to analyze, 2…

Normalization probe limma gcrma Normalization probe limma gcrma

updated 20.0 years ago • Jenny Drnevich

block effects, but TMM and friends all assume near-constant expression across the design, which is violated by our (nuisance) block-level differences in composition. We see this when we compare edgeR TMM-normalized log(cpm

Normalization edgeR Normalization edgeR

updated 13.2 years ago • Aaron Mackey

and the values \delta h for differential expression (equivalent to the difference between the log-ratios if using rma()) are both on the wrong scale. Well, as rma() and other methods use log-transformed data, but vsn() uses a different...tranformation, I think using expresso() to calculat vsn-normalized measures seems to log- AND arcsin-transform the data. Is there a way around that? From the des…

affy vsn affy vsn

updated 23.0 years ago • Oliver Hartmann

<div class="preformatted"> FYI, The change log appears to be blank. http://www.bioconductor.org/changelog.html Thanks, -Steve This e-mail, including any attachments, is...div class="preformatted"> FYI, The change log appears to be blank. http://www.bioconductor.org/changelog.html Thanks, -Steve This e-mail, including any attachments

updated 21.4 years ago • Roels, Steven

div class="preformatted">Hello, I am searching for a cDNA spike-in data set that is public available. Is anyone on the list aware of such a dataset? Thanks! Peter</div

updated 21.0 years ago • Peter Sørensen (HAG)

div class="preformatted">Hi all, How can I compute the logs of the Affybatch data? Stephen.</div

updated 22.3 years ago • Stephen Nyangoma

tree structure, in particular the branch nodes are shown.   ![](https://upload.wikimedia.org/wikipedia/commons/thumb/3/3f/NewickExample.svg/654px-NewickExample.svg.png) The example is from wikipedia (https://en.wikipedia.org

ggtree lineage

updated 9.3 years ago • yun YAN

function of DESeq2, when estimating dispersion alpha, I think the function is optimizing alpha on log scale (i.e. take the partial derivative with respect to log(alpha)). My questions are: 1. Why not optimizing alpha on original...scale? 2. Optimize alpha on log scale vs. optimize alpha on original scale, do we get the same optimal alpha? Thanks.   <embed height="0" id="xunlei_co…

deseq2 dispersoin estimatedispersions

updated 7.7 years ago • xr2120

I'm using the flowCore package coming from BioConductor. No i would like to do a transformation, a log tranformation. Although i think i put everything like it should, i get this error: Error in log(x, logbase) : Non-numeric argument

flowCore flowCore

updated 12.9 years ago • Pieter Coussement

gene identifier. Loading detected dataset hsapiens_gene_ensembl ... 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 PUBLIC, …

goexpress

updated 9.8 years ago • martin.hoelzer