Bioconductor Forum

<div class="preformatted">Dear all, I am analyzing data obtained using the HuGene2.0-st arrays from affymetrix. I have used aroma for preprocessing and limma for diff. expression analysis. After multiple testing I lost significance and therefore I want to filter out genes that do not have a potential to be significantly different. So I have created an expression set after rma plm &l…

Annotation Preprocessing hgu95av2 limma Annotation Preprocessing hgu95av2 limma

updated 12.7 years ago • Andreia Fonseca

<div class="preformatted">I'm trying to get text descriptions of PFAM family names from the PFAM package. I've tried to run the example code from the pfamAC2PDB help. > AC2DE <- pfamAC2DE() > head(AC2DE) $PF00244...<div class="preformatted">I'm trying to get text descriptions of PFAM family names from the PFAM package. I've tried to run the example code from …

updated 17.9 years ago • Daniel Gatti

there's a minor bug in get.psi.code of fitPLM. Here's the function: > get.psi.code function (name) { psi.names <- c("Huber", "fair", "Cauchy", "Geman-McClure", "Welsch", "Tukey", "Andrews") if (!is.element(name, psi.names)) { stop(paste(name, "is...not a valid Psi type. Please use one of:", "Huber", "fair", "Cauchy", "Geman-Mclure", "Welsch", …

updated 17.4 years ago • Paul Boutros

Prepare the 'metadata' data frame ... metadata: OK Now generating chrominfo from available sequence names. No chromosome length information is available. Error in .normargSplicings(splicings, transcripts_tx_id) : 'splicings...cds_start' must be an integer vector In addition: Warning messages: 1: In .deduceExonRankings(exs, format = "gtf") : Infering Exon Rankings. If...this is not what you e…

TranscriptDb TranscriptDb

updated 12.8 years ago • Fong Chun Chan

for a full-time Adjunct or In Residence faculty position at the Assistant or Associate Professor level in cancer bioinformatics. Applicants must possess a doctoral degree in statistics, biostatistics or a closely related...from proposal development through data analyses; provision of bioinformatics instruction at all levels; and pursuit of an independent bioinformatics research program, becoming…

Proteomics Cancer Proteomics Cancer

updated 17.5 years ago • Ru-Fang Yeh

I am using the "org.Ss.eg.db" package to input gene names to my list of ENSSSCG.... > sigs <- readxl::read_excel("C:\\R\\C_vs_F_genes_genelist_Galaxy.xlsx") > sigs.df <- as.data.frame...returned > Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid…

map.ID.to.genenames

updated 3.8 years ago • lucie.eicul

div class="preformatted">Hello, Is there a way to specify/change the significance level, i.e alpha, in ks.test so one can adjust for different alphas for different sample size? -- Shripad Sinari </div

updated 17.6 years ago • Shripad Sinari

preformatted">Dear all, Is there a way with Bioconductor in which I can convert such EnSemBL probe names into the standard gene names? AFFX-M27830_5_at AFFX-M27830_M_at ENSG00000000003_at ENSG00000000005_at ENSG00000000419_at

probe probe

updated 17.2 years ago • Gundala Viswanath

Error in nullp(tr, "sp", id = go_mapping, bias.data = gene_len) : bias.data vector must have the same length as DEgenes vector! How is it possible to fix it? Thank you in advance

edger goseq

updated 8.2 years ago • mictadlo

4 controls). I am analyzing the data using a single channel approach (lmscFit), which I think valid for my dataset, as all channels from each individual nicely cluster together, apart from all other channels. The hybridization...targets2 <- targetsA2C(targets) u <- unique(targets2$Target) f <- factor(targets2$Target, levels=u) design <- model.matrix(~0+f) colnames(des…

BRAIN BRAIN

updated 20.2 years ago • Koen Bossers

Sample_info$Individual, Sample_info$Breed, sep = '.')) Status<-factor(Sample_info$Status, levels = c('Treated', 'Control')) Then I made the 'design matrix' design <- model.matrix(~Animal+Status) which produced a design matrix...that looks like this ![design matrix][2]. My question is why the design matrix named its last column ' StatusControl' and not 'statustre…

R edgeR

updated 3.5 years ago • Mohamed

pre> set <- useDataset(dataset.name, mart=mart)</pre> gives <pre> Error in (function (cl, name, valueClass) : assignment of an object of class "AsIs" is not valid for @'dataset' in an object of class "Mart"; is(value, "character

bug biomart

updated 9.0 years ago • Philip Lijnzaad

code below). I was wondering if anyone has an idea about how to change the default affy-IDs as row names in a KEGG2heatmap (or GO2heatmap) to have gene symbols or gene names for that matter displayed in the heatmap. Changing...c(9,9), col=bluered(256),ColSideColors=groups.color2,cexRow=1.2) ##gives what I expect, with row names written as probeset Affymetrix Ids > matrix_eset_1108_symb…

Annotation GO annotate affy Annotation GO annotate affy

updated 17.4 years ago • Celine Carret

hi, if i have two lists, name A B C and interaction __from   to    InteractionType__ 1        3     0.179539385 2 &nbsp...hi, if i have two lists, name A B C and interaction __from   to    InteractionType__ 1        3   &…

software error R

updated 9.8 years ago • Angel

analysis. In my dataset, several ASVs belong to the same genus but are not identified at the species level (e.g., Acinetobacter sp1, Acinetobacter sp2, etc.). I am considering summing the abundances of ASVs belonging to the same...genus to visualize higher-level taxonomic trends; however, I am not sure if I can do that. Would you recommend performing this type of aggregation (collapsing...counts …

Bioconductor

updated 8 weeks ago • acharyapratiksha24

but has 13 columns, which need manually add a tab at the beggining of the header to make it a valid RMA format__"  library(affy) > data <- ReadAffy() > exp <- rma(data) Background correcting Normalizing Calculating

software error probe affy RMA

updated 10.4 years ago • Angel

<div class="preformatted">Dear Bioconductor Members,  I must start by saying that I'm just starting on analyzing the RNA- Seq data. I have RPKM values and their corresponding P-values for each gene. I wanted to know if I'm correct using " N= RPKM x L x Ntot X 10-9 >where N = number of mapping reads at a given gene locus, L = estimated length (bp) of the gene locus, Ntot = …

convert convert

updated 14.1 years ago • Avinash S

div class="preformatted"> As you guys know, there is a growing evidence showing that a probe- level analysis (as opposed to a probeset-level or a gene-level analysis) could be useful in analyzing Exon arrays. I am currently...chips with the resources at hand and I was wondering if anyone has ever tried to perform probe level analysis using xps. Also, I would be grateful if anyone could point …

probe xps probe xps

updated 14.3 years ago • Lavorgna Giovanni

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updated 17.9 years ago • JONG-MIN LEE

Hi, I am trying to extract results from a DESeqDataSet object based on a customized contrast list. Depending on whether the design contains an interaction term, the effect/result names change, which makes it quite difficult to extract results in an automatic fashion (e.g. as part of a script or app, without checking resultsNames() manually). Here's an example based on ?results: <pre> lib…

DESeq deseq2 resultsnames

updated 9.4 years ago • akaever

Hello. My PI is interested in comparing groups of cells on a cell-to-cell basis using pseudobulking, and our groups have differing numbers of cells. For that reason, I suggested factoring in cell numbers into the normalization process to also generate DE results at the tissue level. To exemplify, I made the following table to simulate some of our data. The example has two groups of cells (A and …

DESeq2 DifferentialExpression differentialex Pseudobulk SingleCell

updated 2.9 years ago • skanda.hebbale

<div class="preformatted">Hello everyone, I have been playing with the GLM approach for RNA-seq data in DESeq and edgeR but I am fairly new in DE analyses. I am interested in pairwise comparisons in multi-factor multi-level designs. My question concerns my understanding of an application of the glmLRT function #My code is >countsTable <- read.delim(file) >header &…

updated 13.0 years ago • Dorota Herman

T>A 1140 T>C 8198 T>G 1830 My concern is, along with the position i want the gene names so is it possible to get the gene names from SigProfilerMatrixGenerator output ? and if not that whats the other way to...get the gene names from VCF files

BioCor StarBioTrek MatrixGenerics

updated 2.2 years ago • karmasstark

DESeq2 offers and suggested gene-level differential expression methods. Using the tximport vignette to import transcript level estimates, __is it okay not...to sum them to the gene level and use the transcript level estimates for DESeq2 standard workflow?__ This would be an additional question in the...maximum booting. I'm trying to analyze the data per tissue first. The codes I used for transcr…

deseq2 deseqdataset transcripts

updated 8.7 years ago • tarun2

blocks of all rows of the alignment to be on adjacent lines.  If they are interspersed with valid \#=GR comments as in HMMER output, it incorrectly surmises the file consists of blocks of one row each and reports an error

biostrings

updated 9.0 years ago • david.huen

Hi, all, Does anybody know some bioconductor packages for the quality control on Affymetrix probe level? Thank you. Cheers. Xin This e-mail is from ArraDx Ltd The e-mail and any files transmitted with it are confidentia...{{dropped

probe probe

updated 20.4 years ago • Liu, Xin

Hi, I want to import data to R with the columns name of these: \#ID  study1cond1  study1cond1  study1con2  study1con2  study2con1  study2con1 &nbsp...nbsp; 0               84  But after importing the columns\` name change to: \#ID  study1cond1  st…

software error deseq metarnaseq HTSFilter columns

updated 8.4 years ago • ed_isfahani

preformatted">Hello I was reading the guidelines at the bioconductor developer page. But how about naming functions? There is a part for "variable names" and the hint for using namespaces. In several packages I found functions...of the kind: "just.rma" Is using the "dot" in a function name permitted and has the "dot" any meaning? Thanks Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwi…

updated 18.3 years ago • Markus Schmidberger

<div class="preformatted">Hi, all; While analyzing Affymetrix data set, when gene-information is necessary after probe-level data analysis is performed, Bioconductor looks for a related CDF package and if it cannot find it locally, it tries to get it from Bioconductor web site and install it. (If this is not correct, please let me know.) My question is this. When Bioconductor tries to inst…

cdf cdf

updated 21.4 years ago • Tae-Hoon Chung

Error in nsc(data$x[gene.subset, sample.subset], y = y, proby = proby, : Error: each class must have >1 sample There is discussion in the documents (http://www- stat.stanford.edu/~tibs/PAM/Rdist/doc/readme.html) about

GO pamr GO pamr

updated 21.4 years ago • Dick Beyer

across three time points when accounting for the within subject variability in DEXseq for exon-level data? In DEXSeq user must specify on the coldata the exon column("this","other") that has to be taken into account. How  can...I implement it/add on the model that I've used with gene-level data on DESeq2? The full and reduced models are described below. Full: ~condition + time …

dexseq timecourse model.matrix model

updated 8.4 years ago • heikki.sarin

lt;-c("A_CONTROL","B_CONTROL", "A_B") contrast.matrix <- makeContrasts(A-CONTROL, B-CONTROL, A-B, levels=design) fit2 <- contrasts.fit(fit, contrast.matrix) fit2 <- eBayes(fit2) write.fit(fit2,results=NULL,"Annotated_fit2_Table.txt...none") When I output this table I have all the statistical data as expected but not the gene names and annotation,etc that the help file says s…

Annotation gcrma Annotation gcrma

updated 19.8 years ago • Quentin Anstee

<div class="preformatted">Hello, I've a problem aligning tickmarks to an image. I've created a correlation matrix for 84 affy mouse chips. I'm visualizing the matrix as an image with colour coding according to the correlation coefficient. The 84 chips are distributed over three factors, but the desgin is unbalanced, so that the tickarks and the lables for the axis are must not evenly dist…

affy affy

updated 21.3 years ago • Arne.Muller@aventis.com

I am trying to know gene names from a heatmap made by heatmap. 2. Since I have many genes, the gene names (row labels) are not readable. I typed following. Please...teach me how to know gene names from heatmap. data <- read.table("sample.txt") data <- as.matrix(data) out\_f <- "cluster2.png" library(gplots) heatmap.2

R

updated 8.5 years ago • nakanomasayuki265

Hello, I am interested in using DESeq2 to analyze a bulk RNA-seq dataset with one factor and 12 levels (control and treatments), and 4 biological replicates per level. I was wondering how using one or multiple input sample...of sample information and then look at the possible pairwise contrasts between control and treatment levels. Alternatively, 2) I could provide multiple sample tables, one fo…

deseq2

updated 7.2 years ago • fl

my interpretation. ``` > library("DESeq2") # make example dataset and fix the reference level > dds <- makeExampleDESeqDataSet(n=10000,m=12) > dds$condition <- as.factor(c(rep("Control",6), rep("Treatment",6))) > dds$genotype...dds) <- ~ condition + genotype + condition:genotype > dds <- DESeq(dds) > results(dds, na…

deseq2 design formula log fold change

updated 5.3 years ago • jason.taotaotan

was hoping that some of the experts that read these posts could comment on it - specifically, is it valid? Is there something I could be doing that is easier/more appropriate? I know it works as I have been getting the genelists...correlation=corfit$consensus) >fit <- eBayes(fit) >cont.matrix <- makeContrasts(AvsB=A-B, levels=design) >fit2 <- contrasts.…

Bayesian limma PROcess Bayesian limma PROcess

updated 15.3 years ago • Orfe, Lisa

hello all, i am doing a differential gene expression analysis using limma, i have 3 conditions S0,S1, and S3. I am creating the contrasts and doing the fit function but its giving the error ( Number of rows of contrast matrix must match number of coefficients in fit) ``` > contrast.matrix <- makeContrasts( + S1_vs_S0 = S1 - S0, + S3_vs_S0 = S3 - S0, + S1_vs_S3 = S…

limma

updated 19 months ago • zzrammal

Dear members: I am struggling to find the gene names for the probes found in the above mentioned microarray chip. I have search in the available annotation packages available...in bioconductor, but the probe names are not present in them. I have also tried wieh biomart but "pd.porgene.1.1.st" is not a valid attribute. Has anyone done

pd.porgene.1.1.st affymetrix microarrays

updated 10.0 years ago • serpalma.v

Hey everyone, I was hoping someone can help me with this: I am currently doing QC analysis of my RNA-seq data which was done in a controlled cell-line (knockdown experiment) and I’m interested in analysing it at the gene and transcript level. I used Salmon in selective alignment mode with 50 bootstraps and imported the data using `tximeta` and performed an initial...cell-line (knockdown exp…

salmon RUVSeq cqn PCA RNASeq

updated 2.6 years ago • ur.n

div class="preformatted">An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070606/ 6510a13c/attachment.pl</div

updated 18.5 years ago • Maurice Melancon

<div class="preformatted">You can do it using one of the programs available in apt-tools from affymetrix (http://www.affymetrix.com/support/developer/powertools/index.affx): apt-cel-extract will extract probe level intensities from cel files. This program memory maps all the cel files from which intensities will be extracted. As a...www.affymetrix.com/support/developer/powertools/index.affx…

probe probe

updated 17.7 years ago • raffaele calogero

I'd like to read in transcript-level results from RSEM using the `` tximport `` package, but this does not appear to be supported. The `` tximport `` vignette only describes...importing `` sample.genes.results `` (gene-level) data, and the `` tximport::tximport `` function is hard-coded to set `` txIn = FALSE `` when `` type = "rsem" `` (see [here](https://github.com/Bioconductor...and Kallisto.…

tximport rsem

updated 8.0 years ago • Patrick Kimes

for example, in the same gene, but we obtained a seemingly correct but actually erroneous expression level for transcripts with high sequence similarity. Therefore, I quantified all the transcripts at the sample level to avoid

DESeq2

updated 4 months ago • 泓朴

Dear goseq developers：       Hello ,my name is Xu,ZhengZheng ,a student of Beijing Institute of Gennomics ,Chinese Academics of Science. After I use edgeR to do difference...Question2:when I use goseq(pwf,"hg38","refGene"),it pop-up code with errors:   ___in names(tmp) = rep(names(map),times=as.numeric(summary(map)\[,:attempt to set an attri…

goseq

updated 10.3 years ago • xdzperfect

div class="preformatted">Hello, Does anyone know if there is a limited number of levels for a factor or how to reset the defaults? I have a two factor experiment which one factor has 2 levels while another has...7 levels. I got errors while I run following analysis. Please help. Thanks, Steve > design <- model.matrix(~phe+tr) > design (Intercept

updated 15.3 years ago • steve shen

is used. I initially noticed this when I tried to annotate the normalized data at the transcript level, which returned only `NA`s when processed through `fitProbeLevelModel`, but when `rma` was used this was not the case. Then...OK Residuals... OK Scale....... OK > > normalized.data.plm Probe Level Model Method..............: plm # Samples....…

oligo HTA2.0 affycoretools RMA fitProbeLevelModel

updated 6.4 years ago • Guido Hooiveld

which would normally be some test to do with a p-value or other score) and to specify allGenes as a named factor, where the probeset is 1 if I consider it interesting, and 0 otherwise. In the code snippet below, `exprset` is an ExpressionSet...is "interesting" and 0 otherwise geneList <- factor(as.integer (all_genes %in% interesting_genes)) # name the factor with the probeset names names (…

Microarray GO topGO Microarray GO topGO

updated 15.3 years ago • Mike Dewar

<div class="preformatted">Dear all, I'm using GRanges objects ('df') to store read counts on 7M genomic regions. I found that the colnames of mcols(df) do not behave nicely when using the names are not 'syntactic valid'. But this behavior depends on whether columns are referenced using '[[' or using '['. I would think this is not intended to work like this? ############### # initialize a …

ASSIGN ASSIGN

updated 11.5 years ago • Ludo Pagie

list, I noticed that GRangesList objects are not allowed to have outer elementMetadata columns with names identical to names of inner elementMetadata columns (see below) Is this restriction necessary? And if yes, should identical...names raise an exception at the time of construction rather than further down the line? Best wishes, Leonard > gr <- GRanges...Error in validObject(…

updated 12.2 years ago • Leonard Goldstein

Stim 1`, `Stim 2`, `Stim 3`, `Stim 4`, ..............., `Stim 10`). Basically, this is a multi-level experiment with multiple samples from each subject, and analysis was perfomed using `multi-level experiments in the...Disease_A_Mild_Stim_1 DbaMS4.1 = Disease_B_Mild_Stim_4 - Disease_A_Mild_Stim_1 etc., levels=design) Thank you, Toufiq

ggplot2 Transcriptomics Visualization R limma

updated 3.6 years ago • mohammedtoufiq91

alphabetToCodes[availableLetters], 0:(length(availableLetters) -  :    'vals' must be a vector of the length of 'keys' > traceback() 7: stop("'vals' must be a vector of the length of 'keys'") 6: buildLookupTable(alphabetToCodes

biostrings

updated 9.7 years ago • Daniel Cameron

hgnc_id", : Invalid attribute(s): entrezgene Please use the function 'listAttributes' to get valid attribute names The error is also happening in the package vignette: https://www.bioconductor.org/packages/devel/bioc...values = keys, : Invalid attribute(s): entrezgene Please use the function 'listAttributes' to get valid attribute names Is this a bug or has the functionality of get…

biomaRt

updated 6.2 years ago • Miguel Juliá

I'm trying to perform normalization on a set of Affy U133A chips. I'm using the affy library on R and was able to do the regular probeset level normalization using ReadAffy() and rma() on the affybatch object. But now I want to do the same thing but for the probe level data. The problem is, I cannot use expresso with summarization disabled (a summary argument has to be provided or it returns an …

u133a normalization rma affy

updated 8.9 years ago • jxd_84

CELfiles is not specified, at least one CEL file must exist in path.\n")) if (is.null(chip.names)) { chip.names <- CELfiles chip.names <- as.character(sapply(chip.names, function...else { if (length(chip.names) != nchips) { warning("Not the same number of chips than chip names. Assigning names from file.\n") chip.names <- CELfiles chip.names &l…

Yeast cdf probe affy Yeast cdf probe affy

updated 20.9 years ago • Joshi, Nina NIH/NCI

If I was just looking at one gene I would use glm with family=bionomial with the expression levels as the explanatory variable. I would like to look at the whole set of genes and for that I would normally use limma, but...limma has the expression level as the response variable and so the binary outcome would be an explanatory variable. Is this an equivalent approach...Is it valid and what are th…

Microarray Cancer limma Microarray Cancer limma

updated 15.7 years ago • Daniel Brewer

and GOstats. The analysis in both cases worked properly, but I would need an enrichment for a higher level of GO (less specific). Is someone aware of a way to select the annotation level to use for performing the enrichment with

topgo gostats go

updated 11.2 years ago • artur

Hi there, I'd like some guidance on how best to carry out differential expression analysis using the limma pipeline with my data set. Below is representative of my targets data.frame: Sample Patient Tissue Time Treatment Class 1 1 Diseased 0 Topical A 2 1 Diseased 2 Topical A 3 1 Diseased 4 Topical A…

limma rnaseq r

updated 5.6 years ago • A.Barden

normalized values. My concern is that running RMA normalization on only 3 replicates is not a valid use of the method. Can anyone offer advice on the number of replicates necessary to run RMA normalization, or if other

Normalization Normalization

updated 15.7 years ago • James W. MacDonald

Invalid attribute(s): encode_region Please use the function 'listAttributes' to get valid attribute names I checked attributes and filters and both valid, according to getAttributes() and getFilters() functions

annotation

updated 5.2 years ago • Zsolt Gyüre