Bioconductor Forum

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mgu74bv2cdf hgu133a2.db

updated 2.2 years ago • WebAsha

for six purified cell types (DMR in Bcell vs else, CD4T vs else, etc), but I have unequal sample sizes in each group: > table(pheno_table$cell_type) Bcell CD4T CD8T Gran Mono NK 4 12 4 14 6 4 My two questions are: (1) Will the unequal...sample sizes be a problem for `dmrseq`? (2) My understanding based on reading the `dmrseq` vign…

dmrseq

updated 6.4 years ago • Stephanie Hicks

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NewWave MMAPPR2

updated 2.2 years ago • WebAsha

12:02:36 +0200 (CEST) From: edoardo missiaglia <edo_missiaglia@yahoo.it> Subject: [BioC] time-course experiments To: bioconductor@stat.math.ethz.ch Message-ID: <20031008100236.12628.qmail@web11701.mail.yahoo.com...between time points. However I have read few papers (such as Peddada et al. Gene selection and clustering for time-course and dose-response microarray experiments using...m…

Microarray Clustering Microarray Clustering

updated 22.2 years ago • Baker, Stephen

have a dataset with two treatments and 4 biological replicates each. This is an amplicon sequencing experiment where all amplicons are the same size, and the total number of amplicons is ~200K. Similarly to a CRISPR, within each...I am assuming that the experimental system is very noisy. A comparison of data between independent experiments suggests that I have many false positives. I have bee…

independentfiltering DESeq2 CRISPR

updated 4.8 years ago • Rubén

Our lab as cumulated many RNA-Seq experiments with the same cell line over the years. We want to take all the control experiments done to estimate the expression...levels of genes in this cell line. Fastq files for all these 8 experiments were processed using Hisat2 and featureCounts to get gene counts. Replicates from each exp vary from 1 to 3. To...the standard deviation to estimate how mu…

RNASeq BatchEffect DESeq2

updated 3.5 years ago • Alexandre

embrionic cells. According to PCA (see below), I have found that samples are clustering according to Experiment day and not by Condition ![enter image description here][1] Then, I have performed in parallel the analysis - taking...all samples - taking all samples and corrected by the batch effect - taking samples processed only at day 27th - taking samples processed only at day…

DESeq2 BatchEffect

updated 2.8 years ago • giulia.lopatriello

<div class="preformatted">Dear Bioconductor users and developers! We have a complex experiment (for me) and we would like to receive suggestions on how to analyse it, if possible. The design is: Var A Var B Var C Var D ------------- ------------- ------------- ------------- T1 T2 T1 T2 T1 T2 T1 T2 Vars A and C are resist…

Genetics Normalization vsn limma Genetics Normalization vsn limma

updated 19.9 years ago • Marcelo Luiz de Laia

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Statistical Modeling Job

updated 10.6 years ago • Doe, Aimee

Hello, I am trying to use the SVA package to obtain values after batch effect removal in RNA seq data (using DESeq rld counts), My design: <pre> design </pre> <table border="0" cellpadding="0" cellspacing...nbsp;               strain batch</td>…

sva combat

updated 10.4 years ago • GFM

cf. https://stackoverflow.com/questions/14589354/struggling-with-integers-maximum-integer-size ```r library("HDF5Array") library("DelayedRandomArray") library("bit64") # This does work (2^31-1 > 1000*1000*1000) dim1 <- c(1000,1000...1000) l1 <- as.integer64(prod(dim1)) darr1 <- RandomBinomArray(dim=dim1, size=1, prob=0.2) tmpfile1 <- paste0(tempfi…

bit64 HDF5Array DelayedArray

updated 4.5 years ago • Koki

IV07/IVbm.htm > ETH, Zurich, Switzerland > July 4, 2007 > > > *** Extended Paper deadline: 15 March, 2007 *** > > Associated and co-located with the 11th International Conference on Infor= mation Visualization...gt; July 4 - 6, 2007 > > CALL FOR PARTICIPATION > > We are soliciting original papers in the area of informati…

Microarray Alignment Pathways Visualization Microarray Alignment Pathways Visualization

updated 18.8 years ago • Vincent J. Carey, Jr.

which inherits from "NChannelSet" (defined in Biobase). You would consider your first round of the experiment as an NChannelSet with N=2 (colours), 3*96=288 rows ("features") and 4 columns (2 for C and 2 for E). You denote the metadata...featureData" slot. There is no off-the-shelf way to use the same instance of an "NChannelSet" for experiments in which people changed the plate configuration m…

cellHTS2 cellHTS2

updated 17.1 years ago • Wolfgang Huber

to mention that even if you do normalize all the chips together, you are still likely to see the 'batch' (or 'block') effects. To try to assess the extent of the problem, you might cluster the samples and see if you get samples from...the same batch clustering together. Best regards, Darlene ------------------- Hello, the 11 tumour sampel are considered as biological replicates, or...subject…

Clustering Cancer Clustering Cancer

updated 21.0 years ago • Darlene Goldstein

Dear Bioconductor List, I am analyzing an RNAseq experiment taken from two different batches. I have encountered a strange voom plot and cannot get rid of it by taking...that the glitch in the first graph is due to batch effects. I then tried batch adjustment in Limma, using batch as a covariate. MDSplot\_bybatch\_log\_no\_correction.pdf...that there is a pronounced …

limma voom batcheffect covariate

updated 8.6 years ago • raf4

<div class="preformatted">> Date: Wed, 30 Jul 2014 22:01:34 +0000 > From: "Rao,Xiayu" <xrao at="" mdanderson.org=""> > To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Subject: [BioC] multi-level design - a simplified question - corrected > table > > Hello all, > > I do need some help…

updated 11.4 years ago • Gordon Smyth

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ScreenR

updated 7 days ago • Maya

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teaching Carpentries

updated 3.1 years ago • Maria Doyle

programming skills (python/perl, R, C/C++) and/or large-scale data analysis skills. Substantial experience in Bioinformatics/ Computational Biology is a plus. However, a non-bioinformatics background with strong training...nihroadmap.nih.gov/epigenomics/). How to apply: Applicants should submit a CV, pdfs of your best papers and name/contact information of three references to Dr. Wei Li (WL1 at …

updated 17.0 years ago • Wei Li

div class="preformatted">Dear Sohail, Well, there are lots of ways to generate such a table. Perhaps the simplest is fitsel <- fit2[sel.dif, ] as.data.frame( fitsel ) Best wishes Gordon >Date: Tue, 20 Dec 2005 14:03...43 -0500 >From: "Khan, Sohail" <khan at="" cshl.edu=""> >Subject: [BioC] Time course experiment.... >To: <bioconductor at=""…

limma limma

updated 19.9 years ago • Gordon Smyth

Hello, Thank you for the creation of the DESeq2 tool! It has been very useful in understanding the requirements and downstream analysis of an rnaseq experiment. At the moment I have a phd student who has a time-course experiment where they have low mapping rates for significant portion of their genes. I would like to check a few things, largely the design formula and potential issues with batc…

RNASeqData DESeq2 RNASeq

updated 22 months ago • island

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ScreenR

updated 7 days ago • Maya

they are insisting on doing the analysis using all samples.  I also tried to do remove hidden batch effect using sva package (got two surrogate variables SV1 and SV2) and re-done the DESeq2 analysis as suggested...all cell lines (the command lines are at the end of this message). However, by removing the hidden batch analysis from my groups of 4 control and 4 carriers, the numbe…

deseq2

updated 9.1 years ago • Leila.Eshraghi

methods is different, could it be imaginable to combine the output of both packages to increase the size of a gene set (so far regardless of stat. questions)? Has someone experience with that issue or experience with witch method

updated 15.8 years ago • Hildebrand, Georg

I am trying to recreate the differential gene expression results from the following paper between Alzheimer’s and normal brain donors (https://genomemedicine.biomedcentral.com/articles/10.1186/s13073...up into normal, low, and high Alzheimer’s based on 6 different categories. The supplementary table 4a from their paper shows the number of differentially expressed probes based on linear regression…

limma microarray differential gene expression linear regression edger

updated 6.8 years ago • ravelarvargas

Hi All, This would be extremely easy in Access, but should be manageable in R too :-) I have two tables, which are the annotation files for two platforms. I have one common identifier, the âprobenamesâ, which is used in both...tables. I would like combine table 1 and table 2 into table 3. The âmatchâ is not good, since it gives only the first match. I have...multiple entries in table 2,…

Annotation Annotation

updated 17.4 years ago • Dr Gyorffy Balazs

5 0.15625 0.05263 The overall.error is (b+c)/(a+b+c+d) from cross-validation for training data; while the overall.pred.error is the one for test data. Since the sample sizes of training and test data are different...it gives me the result which performs better in test than training. I am wondering if there are some other metrics to evalute this classification error rate so that it can cons…

updated 19.0 years ago • Weiwei Shi

Hello, I tried to search for a correct answer, but I don't think I've found one. I have an experiment with paired samples, I've performed DESeq2, and now I would like to plot DESeq2 normcounts. All the discussions...Hello, I tried to search for a correct answer, but I don't think I've found one. I have an experiment with paired samples, I've performed DESeq2, and now I would like to plot DESeq2 n…

DESeq2

updated 18 months ago • altuda

I trying to add some interactions to my DESeq2 design matrix. My 12 samples are divided into two batches. There are two strains. These samples are coming from 6 individuals, so it's also a paired experiment with two treatments...rownames(rawcounts) <- c(paste0("gene", 1:no_of_genes)) # Create metadata for the dataset batches <- c("a","a","a","a","a","b","b","b","b","b","b","b") …

DESeq2

updated 2.3 years ago • lamia11me

Hello, I have used DESeq2 to find genes where the expression level correlates with the size of a continous variable - in this case, the number of cells in a population (pop). We noticed that we have a batch effect in our...data depending on what day we processed the experiment (day). So my design set up was as follows: >cData=data.frame(day=as.factor(df$day), pop=df[,x]) >row…

deseq2

updated 6.6 years ago • Edie Crosse

<div class="preformatted">This note is to gauge the level of interest in a two-day Bioconductor training course to be held in Boston mid- or late May 2003. Details of syllabus will depend on the enrolling population, but will...div class="preformatted">This note is to gauge the level of interest in a two-day Bioconductor training course to be held in Boston mid- or late May 2003. Detai…

Preprocessing Infrastructure oligo Preprocessing Infrastructure oligo

updated 22.8 years ago • Vincent Carey

perform time series analysis like a one-way ANOVA on multi-groups of samples,but there is a obvious batch effect in my data . I would like to generate a single p-value that indicates difference among the time without batch effect...and this is my coldata: - List item sample condition batch 2h_1 2h one 2h_2 2h one 2h_3 2h one 2h_4 2h two 2h_5 2h two 2h_6 2h two 4h_1 4h one 4h_2 4…

deseq2 time series remove batch effect

updated 6.8 years ago • Nicola

example, I have all tumor samples from batch1 and all normal samples from batch2. How do I perfrom batch correction here? In my case, where group (tumor vs. normal) and batch (batch 1 vs. batch 2) are fully confounded, traditional...batch correction methods like ComBat or limma's removeBatchEffect may struggle. @mikelove

limma DESeq2 BatchEffect

updated 14 months ago • Bioinformagician

Hi everyone, I am using edgeR to identify differentially expressed transcripts based on a simple RNA-seq setup (tumor vs control samples). The *DGELRT* object with results provided by edgeR contains, among others, logFC values calculated for the contrast that I used (Tumor vs Control). I additionally need the average read counts for both sample groups, used to calculate the logFC values. For…

edgeR batch-effect RNA-seq read counts ngs

updated 6.9 years ago • Roman

levels: normal, tumor (where normal is the base level). Then results(dds) will build a result table for tumor vs normal, controlling for the patient effect. ``` Here is my colData: ``` colData(dds_matched) DataFrame with 144...design =~ sample_type+patient) dds_DE_matched <- DESeq(dds_matched) estimating size factors estimating dispersions gene-wise dispersion esti…

DESeq2

updated 4.8 years ago • xiaofeiwang18266

I have read this paper (https://academic.oup.com/nar/article/40/10/4288/2411520?login=false) and got interested in understanding a little bit...for each abundance quantile bin and a BCV for each gene based on some middle ground for low-sample-size experiments. The idea is to identify mean differences regardless of differences between extra-Poissonian mean-dependent...and/or option in the package …

edgeR

updated 10 months ago • James

Dear all, I'm learning to perform meta-analysis of affymetrix microarrays. I tested 4 studies with package geneMeta. The sample sizes of the 4 studies are very small: <table border="1" cellpadding="1" cellspacing="1" style="width:500px"> <tbody> <tr> <td> </td> <td>Cases</td> <td>Controls</td> </tr> <tr&…

preprocessing microarray genemeta

updated 9.2 years ago • Lian Liu

are sorted into two related types say A and B. These samples are sequenced using 10X in the same batch/run. For practical reasons we cannot assay cells from different individuals in the same batch. Cell type A is of greater...total). This seems to fit the rationale for MnnCorrect fairly well in that we wish to correct for batch effects when the experimental design confounds batches with individ…

single-cell scran mnncorrect rnaseq

updated 7.0 years ago • John Reid

induction (Class) even if the inducers are different compounds for different experiments (treatments). I think technically it is possible, but is it conceptually and/or statistically correct? The two...experiments have different design especially the ratio of treated/untreated samples and high batch variability (eg row...control samples for gene 5). ``` Treatment Gene_1 Gene_2 Gene_…

deseq2

updated 5.2 years ago • Sedlin

hi all, i'm interested in building a table of counts from BAM files produced by a PE RNA-seq experiment, for RepeatMasker annotations. essentially to know how many...from the [GenomicAlignments](http://bioconductor.org/packages/GenomicAlignments) package to build a table of counts from gene annotations, which i find it convenient because the input is a 'TxDb' object and the output is a 'Summariz…

GenomicFeatures repeatmasker GenomicAlignments

updated 8.1 years ago • Robert Castelo

Hi, I'm currently exploring methods for batch correction with my RNA-seq dataset from a series of clinical samples. The goal of this approach is to remove batch effects...we see patients separating predominantly by PC1 and batch separating on PC2 . The "removeBatchEffect()" command in limma appears to correct for batch effect very well, with the 5 samples...from each patient now clustering very …

limma batch effect rna-seq

updated 7.2 years ago • Mike A

Hi all, I am conducting some RNA-Seq experiments to determine differentially expressed genes after treatment with various antimicrobials.  I have used...RUVSeq to remove a batch effect present in my data set and DESeq2 to estimate differential expression. I used the EDASeq::plotPCA function on...analysis techniques in the DESeq2 vignette to compare my data before and after removing the…

deseq2 ruvseq rna-seq batch effect

updated 8.1 years ago • dbouzo

<div class="preformatted">If you are only planning on doing rma or gcrma, you might take a look at justRMA and justGCRMA, which use much less memory. I was just informed off-list that you can do 116 of the hgu133plus2 chips with 1 Gb RAM using justRMA. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CC…

Microarray Normalization Cancer hgu133plus2 probe affy gcrma PROcess Microarray Cancer

updated 21.5 years ago • James W. MacDonald

I want to remove a known batch effect with limma using blocking. My experiment has 36 samples from 3 donors with 12 different treatments. The batch...I want to remove a known batch effect with limma using blocking. My experiment has 36 samples from 3 donors with 12 different treatments. The batch effect is based on the different donors. I would like to remove batch effect and later compare diff…

limma batch effect

updated 10.4 years ago • Jeannette

168hpi",3),rep("18hpi",3),rep("24hpi",3),rep("48hpi",3),rep("96hpi",3),rep("168hpi",3)) > batch = c(c("b","c"),rep(c("a","b","c"),16)) > batch = factor(batch) > grouping <- factor(paste(plant, fungi, time, sep=".")) > table(grouping) grouping MK.26.usp...gt; design = model.matrix(~ condition, samples) > design &lt…

edger RNA-seq anova

updated 9.7 years ago • xiaoaozqd

with normalizing my Affymetrix microarray data. We are using Affymetrix Zebrafish Genome Array. The experiment design includes three treatments, namely A, C and G. We have three biological replicates for each treatment, thus...A1, A2, A3, C1, C2, C3 and G1, G2, G3. A1, C1 and G1 were from the first batch (microarray experiment was performed earlier). A2, A3, C2, C3 and G2, G3 were from the secon…

Microarray Normalization Clustering zebrafish probe gcrma Microarray Normalization probe

updated 16.8 years ago • Jun Yin

so even though it's rather unbalanced, there's not much we could do. These are the \# of samples: <table border="1" cellpadding="1" cellspacing="1" style="height:154px; width:172px"> <thead> <tr> <th scope="col">Stage</th> <th scope="col">Total...2</td> <td>44</td> </tr> <tr> <td>3</td> <td>36</td> </tr…

limma complex-design paired design

updated 7.7 years ago • ML18

two plates. I have bulk RNA-seq data with conditions diseased and healthy. One plate from each batch consists of 50 per cent healthy and 50 per cent diseased. I am trying to correct for the batch effect of two plates in Deseq2...both plates. Is there a way to do this I am not aware of? Or do I just use the PCA to see if the batch correction has been done correctly? I use design = plate …

BatchEffect DESeq2

updated 3.5 years ago • lmrogers34

LS_N, NL_Y, LS_Y design<-model.matrix("~0 + grp + age + sex", data=DGE.cpm$samples) # the design table will have columns as groups above, plus age and sex columns. contrasts_table = makeContrasts( LS_B.vs.NL_B = (grpLS_Y...amount of DEGs (up 1829 | nondiff 6711 | down 2374). The problem was that I didn't include **+batch** to my model matrix formula, and there was **one** sample from …

limma

updated 2.2 years ago • Jonathan

to a viral infection. Briefly, both human and viral RNAs were quantified, and as can be see in the table below, reads from viral RNA (= 10 genes) make up ~50% of the entire library in the infected condition. When running DESeq2 on...this dataset, the estimated size factors effectively double the counts for cellular RNAs because they capture the trend of the 20.000 human genes, however...…

deseq2 normalization sizefactors

updated 7.9 years ago • René

So recently we have got sample back with the following design <table border="1" cellpadding="1" cellspacing="1" style="width:500px"> <tbody> <tr> <td><strong>Condition</strong></td> <td><strong>Treatment...td> <td><strong>Lane</strong></td> <td><strong>Batch</strong></td> <td><strong…

deseq2

updated 10.0 years ago • choishingwan

My experimental design is the following: <table border="1" cellpadding="1" cellspacing="1" style="width:500px"> <tbody> <tr> <td>Replicate</td> <td>Tissue_type</td> <td>Genotype</td> </tr...My experimental design is the following: <table border="1" cellpadding="1" cellspacing="1" style="width:500px"> <tbody> <tr> <td&…

deseq2 bioconductor bioinformatics statistics

updated 7.0 years ago • casikecola

package. For now I'm focusing on the ROAST procedure and reading the paper by Wu et al. (_ROAST: rotation gene set tests for complex microarray experiments_, 2010) I've learned how the gene set statistics...are defined (theoretically). For having some doubt about what was intended (in section 3.3 of the paper) for "weighted mean" (were the weights considered only in the numerator or in the denom…

limma roast statistics source code gene set testing

updated 7.3 years ago • Andrea Carenzo

Dear BioC community, I am analyzing microarray data from three different batches. There are many technical and biological replicates in the batches. In the past, when I had only two batches, I was using...removeBatchEffect function from limma, giving the batch of each sample as argument (with batch=...). I am not sure if this function works with more than two batches... I am alerted because...th…

microarray limma removebatcheffect()

updated 9.5 years ago • Eleni Christodoulou

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ScreenR

updated 7 days ago • Maya

div class="preformatted">Hey all, 1. For statistical tests there are usually minimal group sizes recommended for appropriate working. For a chi-square test as example the lower level was 10 obersvations in each field...of the table, if I remember correctly. What about permutation tests? Is there some kind of minimal recommendation for group sizes

updated 18.1 years ago • Benjamin Otto

Hello, To simplify the description of my problem, I will use the same variables as in Example 3 of ?results in DESeq2. I have the following samples from 2 genotypes (I and II) treated under 2 conditions (A and B) <table border="1" cellpadding="1" cellspacing="1" style="width:300px"> <tbody> <tr> <td>sample</td> <td>genotype</td> <td>condition</…

deseq2 replicates

updated 8.9 years ago • le2336

classify eDNA sequences against various databases. For large databases, for example MIDORI or BOLD, training takes very long, often several days. Is there any way to speed this up, short of reducing the iterations (I use 3)? I removed

DECIPHER idtaxa

updated 2.4 years ago • Till

https://biocasia2021.bioconductor.org/) On behalf of the BioC Asia 2021 Organising Committee, we very much looking forward to seeing you online

Workshop Asia BioCAsia Conference

updated 4.2 years ago • Peter Hickey

gives different batches equal weights when combining the results from each batch, even if batches contain different number of samples, am...I right? Additionally, most of my batches contain both treatment1 and treatment2 samples. Let's call these dual-treatment batches. However, a few batches unfortunately...only contain treatment1 samples (or only treatment2 samples). Let's call these uni-treat…

limma batch effect

updated 8.9 years ago • jalali4