Bioconductor Forum

div class="preformatted">Hi, I would like to extract gene names (featureNames) using annaffy, but i am unable to find Affymetrix probe sequence and annotation data for Human Gene...packages/2.3/data/annotation/html/hugene10 st.db.html (CEL files belonging to human gene 1.0 st array) rawdata<-ReadAffy() symbols<-aafSymbol(featureNames(rawdata),"hugene10st.db") I could successfu…

Annotation probe annaffy Annotation probe annaffy

updated 17.3 years ago • Chandra Sekhar

steps as suggested in the limma manual (hence not printing the code) to predict differential gene expression in Tumor samples compared to 19 Normals. Tumors: There were six biopsies from a colorectal cancer patient...and all of them were sequenced using the same protocols. Normal: These are 19 distinct normal tissue ( i.e only 1 sample per tissue type. 1-heart, 1...most part DEG analysis worked,…

limma RNASeq voom DifferentialExpression

updated 3.5 years ago • ACTG_&_beyond

div class="preformatted">Dear all, ? I?have?identified two lists of differential expressed gene?from the same expression data?but treated with different normalisation methods. List A contains?995 genes and list B...contains 2400 genes. More than nine hundreds genes?are overlapped between two lists, namely?most of genes in list A are also included?in list...am wondering is there any other stati…

updated 16.0 years ago • qinghua xu

<div class="preformatted"> Dear list members, We have identified 300 genes response to a treatment in our model by cDNA microarray. We have annotated most of these sequences and signed them with different GO terms. Based on literature searching, we believe that these genes can be categorized to several groups such as: Proteinbiosynthesis (Translation), Metabolism, Protection against react…

Microarray GO Microarray GO

updated 17.3 years ago • ziping zhang

Seq using kallisto and now I want to read the kallisto files using tximport for DESeq2 analysis. My abundance files have identical transcript id for each species but the transcript lengths differ due to differences in gene...lengths in diferent species. When I try to read the files using Tximport I get following error. <pre> > sample <- read.table("samples.txt...sample$sampl…

kallisto tximport RNA-Seq across species

updated 8.6 years ago • urjaswita

the attached four sites we are interested in. I am also wondering is there any limitation on length of the input sequence, for example can we ask CRISPRseek to find all good targeting sites throughout chromosome6 or...CRISPRseek/ErikSontheimer/inputSeq.fa" outputDir <- getwd()   There is no limitation on length of the input sequence as long as you input the sequence as…

CRISPRseek gRNA searching offtarget analysis NmCas9

updated 10.6 years ago • Julie Zhu

Hello, I want to find gene on chromosome 6 using __TxDb.Hsapiens.UCSC.hg19.knownGene__ package, and I use two different methods, but the genes...gt;txdb </pre> and find gens at chromosome 6 <pre> transcriptsBy(txdb,by='gene')->ts ts[seqnames(ts)=='chr6']->onchr6 onchr6[elementNROWS(onchr6)>0]->onchr6 length(onchr6) ####1207 genes on chromosome 6...…

txdb.hsapiens.ucsc.hg19.knowngene txdb

updated 9.4 years ago • li lilingdu

it under certain conditions. Type 'license()' or 'licence()' for distribution details.   Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors...Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help > workflowInstall("sequencing") Warning: unable to access index for repository h…

rnaseqGene genomic sequencing

updated 10.2 years ago • virctoalgn

Does anyone have any experience using emPAI values for differential testing of protein abundances? I was asked to analyze a fairly complex proteomics data set - 90 samples total, 15 males + 15 females, each measured...35938). The funny thing is that emPAI itself is an exponential transformation of the Protein Abundance Index (10^PAI - 1), which is supposedly a ratio of the observed peptides / ob…

proteomics limma

updated 9.4 years ago • Jenny Drnevich

method `generateNull` from your package `singscore` and your NK cell signature from your paper "A gene signature predicting natural killer cell infiltration and improved survival in melanoma patients" (Cursons et al, 2019...singscore/15/534856777 Could you tell us how we can perform `generateNull` with only one set of genes list? Thanks, Tiphaine

singscore generateNull

updated 5.0 years ago • tiphaine.martin

preformatted">Hi, I have got an error while i have been running goseq R package using UCSC known gene ID such numbers, 1,2,...27315.(27181 genes). When i computed pwf. it was fine. but, In getgo function, there is an error message like...gt; head(genes) 1 2 3 4 5 6 0 0 0 0 0 0 > str(genes) Named int [1:27181] 0 0 0 0 0 0 0 0 0 0 ... - attr(*, "names")= chr [1:27181] "1" "2" "3" "4" …

GO goseq GO goseq

updated 15.8 years ago • sunghee OH

<div class="preformatted">Hi, I realized that subsetting an IntegerList object (and probably other IRanges list objects) by the list names plus replacing list element values behaves unexpectedly (at least for me) when the list is not sorted by its element's names. Here a short example: > IL <- IntegerList(chr2=5, chr1=10) > IL CompressedIntegerList of length 2 [["ch…

updated 14.2 years ago • Manuela Hummel

<div class="preformatted"> Dear All, I am trying to use next-generation sequencing platforms to profile gene expression patterns during embryogenesis in our fish model (about 36 different stages). The genome of our model is about 2000 Mb. Currently only a draft of the genome with 70% coverage is available. I am considering using the following strategies to carry out our project: 1. U…

Sequencing SAGE Coverage Sequencing SAGE Coverage

updated 15.5 years ago • Ziping Zhang

<div class="preformatted"> Hi, I am putting a little script together to look at promoter regions, search for CpG islands etc, given a list of gene ids. I thought I would be able to use biomaRt to retrieve the sequence of interest, but I just can't find how right now... either I'm too tired (possible) or I'm missing something and it's just not possible. In particular 'getSequence' looked p…

Transcription biomaRt Transcription biomaRt

updated 19.3 years ago • J.delasHeras@ed.ac.uk

I want to annotate gene names for a segmented file by finding overlap with it with a reference file. Would like to know how can it be done...1" cellspacing="1" style="width:500px"> <tbody> <tr> <td>Chr</td> <td>Start</td> <td>End</td> <td>Gene</td> </tr> <tr> <td>1</td> <td>5930500</t…

annotation

updated 10.6 years ago • seeker

gordonsmyth I am working on differential expression analysis to identify a set of genes that shows significant expression difference between maize lines. Most of the current packages for differential...expression analysis are designed to model expression analysis assuming the gene length is the same across samples. But since I am working with genes from two different maize lines, the gene length …

RNA Normalization

updated 4.7 years ago • nancy

scaledTPM",varReduce=F, txOut = F,tx2gene=tx2gene,ignoreTxVersion = TRUE) > names(rep) [1] "abundance" "counts" "infReps" "length" [5] "countsFromAbundance" # From this point on, I have a difficulty on how to use these

tximport

updated 5.1 years ago • Themis

extract the subset of samples for reference properly. Since the CnChipEffectSet is a list of two enzyme set, how do I extract out the subset of samples for both enzymes I have also listed the error I get below: Here is the code...Chip type: Mapping250K_Nsp,monocell Number of arrays: 80 Names: AA-HGG024, AA-HGG045, ..., OT-HGG155 Time period: 2010-07-14 15:46:23 -- 2010-07-14 15:46:40 Total fil…

updated 15.5 years ago • Manisha Brahmachary

vcf, txdb, seqSource=SEQ_FN) ``` where the _FN files are paths to files on my system. Most of the examples I have seen so far have been with human data (i.e., hg19 or hg38). So, I'm not sure if my usage above is correct. With...x, suggest.trim = TRUE) : GRanges object contains 2 out-of-bound ranges located on sequence 2259. Note that ranges located on a sequence whose length is unk…

R VariantAnnotation

updated 3.3 years ago • rwan.work

contains="GeneIdentifierType", prototype=prototype( type=new("ScalarCharacter", "Uniprot"))) # but the default constructor in that hint is too simple & does not support the annotation argument which is crucial...types: UniprotIdentifier <- function() new("UniprotIdentifier") UniprotIdentifier() # geneIdType: Uniprot # make a geneset up <- c("Q9Y6Q1", "A…

Annotation Cancer hgu95av2 convert GSEABase Annotation Cancer hgu95av2 convert GSEABase

updated 14.4 years ago • Mark Cowley

T, sep="\t') note: phenodata.txt is a text file with variables in columns and samples number and/or names in rows. The output file appears to have the correct number of cases (133) and variables (20) Then I create a file, x, that has...all the CEL file names. Then I attempt to create a Affybatch using justRMA: Data1 <- justRMA (sampleNames=x, phenoData=pD1) The output file, a matrix.…

Genetics Genetics

updated 21.8 years ago • Joshi, Nina NIH/NCI

Sergii, You only give a start position, and biomaRt needs a start and end position and a chromosome name if you want to retrieve all genes located in a specific region. An example would be: getBM(c("entrezgene","chromosome_name...is not advisable when using biomaRt. An alternative is that you retrieve all entrezgene ids and the gene start and stop positions and chromosomes from all genes and t…

biomaRt biomaRt

updated 17.8 years ago • Steffen

Dear all, I would like to use `DESeq2` to do differential abundance analysis of the cell clusters from my CyTOF data. Previously, I have tried `diffcyt`, which use `edgeR`. However, I often

deseq2 mass cytometry CyTOF

updated 5.3 years ago • mikhael.manurung

Hi, I am relatively new to bioinformatics, but so far both the paper and the vignette have been very clear. However I still have a question since I am using the DESeq2 package for data other than bulk RNA-seq data. I am trying to use the DESeq2 package for analysis of bulk methylation sequencing data. With the mouse model I am using methylation should correlate to RNA expression upon admin…

DESeq2

updated 2.9 years ago • a.puchkina

same time point. Half the individuals from each treatment (both control and exposed) were run on one sequencing machine (without paired-end reads) and the second half were run at a later date on a different sequencing machine...I analyze the two datasets separately (1 dataset from each machine), I end up with 172 identified DE genes from dataset 1 (FDR p-value < 0.05) and 874 DE genes from…

deseq2 edger

updated 6.0 years ago • christ99

I have  a list of proteins (only `` Uniprot IDs ``) and I am interested in discovering relations between them.   Most importantly I want to focus on disease pathways...analysis, simple category/class of protein, etc. can be helpful too. But disease pathways are the most important analysis for me.   I have two groups of patients and the proteins of interest are absen…

protein disease pathway analysis pathways

updated 7.5 years ago • ረ

1.1056984 1.1096023 My question: Using annotation package how can I convert the probe ID's to Gene names. how do i incorporate gene name in place of 100_g_at? 2. How can I choose/filter P-values from T-test that are less than...0.01 to 0 ? 3. How can write the values into a table with 3 colnames: Gene, P-value, Fold change I am doing this for first time. Please help me. Thank you. Regards…

Microarray Annotation Cancer annaffy convert Microarray Annotation Cancer annaffy convert

updated 21.4 years ago • James W. MacDonald

Dear all, I am trying to map gene names to x y coordinates of probes in celfiles. My celfiles belong to gpl1339(S.aureus). I have some gpl1339 annotation

microarray probe

updated 10.8 years ago • nazaninhoseinkhan

Hi  I am using GOSemSim package for GO similarity calculation. I have a list of Uniprot gene IDs. My dataset is S. cerevisiae. so I code as below: <pre> hsGO2 <- godata('org.Hs.eg.db', keytype = "UNIPROT", ont="MF...computeIC=FALSE) genes <- c("P25044", "P40454", "P32901", "P43606") mgeneSim(genes, semData=hsGO2, measure="Wang", combine="BMA", verbos…

gosemsim similarity

updated 7.6 years ago • ahatashkar

Hello, I use GOseq quite often for RNAseq analyses, including the length bias correction. My question is how to use it properly for data without length bias, e.g., for microarrays. Normally, with...Or do I also have to feed the `` nullp ``function with dummy values (let's say 100 for each gene)? Thanks for your advice! Ben &nbsp

goseq

updated 10.0 years ago • b.nota

below compare to the example.) <pre> > txt <- paste0("##gff-version 3", "\n##sequence-region ctg123 1 1497228", "\nctg123\t.\tgene\t1000\t9000\t.\t+\t.\tID=gene00001;Name=EDEN", "\nctg123\t.\tmRNA\t1050\t9000\t.\t+\t.\tID...Vitis vinifera", taxonomyId=29760, chrominfo=data.frame(chrom="ctg123", len…

maketxdbfromgff genomicfeatures

updated 9.7 years ago • TimothéeFlutre

and plot them using the ALL dataset.  Specifically a linear model for the effects of age on gene expression.  Up to this point I've only been able to develop a model for 1 individual gene (probe id) but because my R syntax...I was able to construct something that looks pretty close to what I'm seeking (but just for one gene): <pre> edata=as.data.frame(exprs(ALL)) edat…

bioconductor ALL linear model

updated 7.4 years ago • detroit.drive

div class="preformatted">I have gene file in this format, everything in one column (no spaces at all): SFTPB|NM_000542.1|4506904|surfactant, pulmonary-associated

convert convert

updated 20.2 years ago • Narendra Kaushik

read length does affect the performance but I'm working on that. In the command line, note that I removed the argument 'format' as bam...default. Since you're using 'bam', the arguments chr.sizes is not necessary either as the chromosome lengths are extracted from the BAM file. Using the chr.map is not necessary for Dmelanogaster as easyRNASeq should correctly...convert the chromosome names. To …

Annotation Organism BSgenome convert BSgenome easyRNASeq Annotation Organism BSgenome

updated 13.5 years ago • delhomme@embl.de

have a venn diagram obtained from Limma using decideTests() default and I would like to extract the gene lists specific for each contrasts. Here is what I did: >matrix <- read.csv("cells-HumanDB.csv") ##columns 1 and 2 are gene names...and uniprot labels, numerical values start on column 3 >design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,4,4,4,5,5,5,6,6,6))) &a…

limma affycoretools limma affycoretools

updated 17.2 years ago • Celine Carret

What is the most efficient usage of voom in a scenario where more batches are arriving at some time in the future? If voom is applied to...What is the most efficient usage of voom in a scenario where more batches are arriving at some time in the future? If voom is applied to each...Batch 1 Batch 2 Sample 1 Sample 2 Sample 3 Sample 4 Sample 5 Sample 6 Gene 1 8.75 …

limma voom Batch Effect Correction

updated 8.7 years ago • Dario Strbenac

exon_number") extracting transcript information Estimating transcript ranges. Extracting gene IDs Processing splicing information for gtf file. Prepare the 'metadata' data frame ... metadata: OK Now generating chrominfo...from available sequence names. No chromosome length information is available. Error in .normargTranscripts(transcripts) : values in 'transcripts

TranscriptDb TranscriptDb

updated 12.7 years ago • Dario Strbenac

I've used BiomaRt to map Ensemble to Entrez Id's and Uniprot Accession Id's . Recently, biomart made some changes and it seems that Unimart is no longer available? If i try this code...that was working before), i get: <pre> mart = useMart(biomart = 'unimart',dataset='uniprot',verbose = T) Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the U…

biomart uniprot unimart

updated 10.1 years ago • john

using Affymetrix U133A/B chips and have been in the process of setting up a database of probe/sequence information and other annotation information (mysql), and learning to use the various R packages. Looking over the...probe sequences and putative gene sequences that affymetrix provides on their website, it is clear that many of the probes are nonspecific...e.g, they perfectly match portions of…

probe PROcess probe PROcess

updated 23.4 years ago • Jeff Sorenson

of 0.88 for the 'back' and -6.53 for the front. Do I interpret correctly that this feature is more abundant in "back" feature 2 (ending iwth ....15db) has a rab.win.back value of -6.9 and a rab.win.front value of 1.94. Do I interpret...correctly that this feature is more abundant in "front"? So the higher the 'rab.win.back' value, the higher the presence of that feature in the treatment? …

MicrobiomeData ALDEx2

updated 3.1 years ago • RvH

DESeq on the two groups to generate a results table. Because the samples have been collected and sequenced at different time in the past 5-6 years, I have included a `batch` variable in the design formula, like below: ``` dds <- DESeqDataSetFromMatrix...design = ~ batch + group) ``` Where for `batch` I used the different sequencing run. Here is an example of the `metadata`: ```…

deseq2

updated 5.7 years ago • alallo

Dear All, I'm analysing my RNASeq data using WGCNA to identify genes that are co-expressed and detect modules, correlating with traits. I have done most of the analysis and identify the modules...traits successfully. Next is to generate a summary, which contains modules with their corresponding gene ID/name and statistics. I have normalized count data from DESeq2 with row for genename and col…

RNASeq WGCNA

updated 4.2 years ago • synat.keam

Hi, I have been trying out the 'cydar' package for testing for differential abundance in mass cytometry data, which was published a few months ago (Lun et al., 2017, Nature Methods). In order to evaluate the...to demonstrate negative values for cell assignment indices assignments <- cellAssignments(cd)[[5]] length(assignments) # [1] 77 head(assignments, 10) # [1]   &nbs…

cydar

updated 8.5 years ago • Lukas Weber

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updated 18.8 years ago • Lana Schaffer

<div class="preformatted">Hi Herve, I need to obtain sequence data for a set of given coordinates. Do you know whether Zv7 (zebrafish) sequence data will be made available for Bsgenome package? Thanks! Best regards, Julie ******************************************* Julie Zhu, Ph.D Research Assistant Professor Program Gene Function and Expression University of Massachusetts Medical Schoo…

updated 16.5 years ago • Julie Zhu

as file "mature.fa" that can be downloaded from MirBase for Homo Sapiens miRNA identifiers and sequences. Whereas dataset "hsTargets" contains all target genes for Homo Sapiens miRNAs listed in file "mature.fa" but also...My purpose is to gather all Homo Sapiens validated miRNAs together with their relative target genes 3UTR sequences, Therefore, if I am guessing right, I can as well use Homo…

miRNA Homo sapiens biomaRt microRNA miRNA Homo sapiens biomaRt microRNA

updated 16.2 years ago • mauede@alice.it

lt;- read.gmt("c2.cp.v7.2.symbols.gmt") pathway.notch.sets <- pathway.sets[grep("NOTCH", names(pathway.sets))] indices <- ids2indices(pathway.notch.sets, fData(eset.filtered)$SYMBOL) set.size <- sapply(indices...FUN=length) indices2 <- indices[set.size >= 10] res <- mroast(eset.filtered, indices2, design=design, contrast=2,nrot=10000) head...My…

mroast camera gene set testing

updated 5.3 years ago • svlachavas

in PLoS Biology documents sample specific biases in differential expression analyses related to gene length: [Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias][1] By using

RNASeq tximport

updated 6.1 years ago • abf

Hello, I am working with some paired-end data, and based on the fastQC reports the R2 reads have pretty bad GC, frag length, and base-pair results. I am worried that using these R2s will add bias related to the issues above. First, I tried just using...with some paired-end data, and based on the fastQC reports the R2 reads have pretty bad GC, frag length, and base-pair results. I am worried that…

alpine deseq2

updated 7.5 years ago • harry.smith

I get the following error message: > as("myArrayLM", def); Error in methodsPackageMetaName("C", name) : 'The name of the object (e.g,. a class or generic function) to find in the meta-data' must be a single string (got an object of class...matrix") In addition: Warning message: the condition has length > 1 and only the first element will be used in: if (is.na(i)) { > …

limma limma

updated 20.3 years ago • Cyrus Harmon

I'm trying some first-pass exploratory analyses of a DESeq2 dataset using vidger. Naturally, I get an error with my very first graph. I created the dataset using tximport, and did a basic analysis: ``` deseqdat&lt...the DESeq2 pasilla dataset example, but not for my own data, which gives an error: ``` Error in names(ls.mean) <- sapply(nam, paste) : 'names' attribute [2] …

vidger

updated 5.6 years ago • bbj23

new Ensembl marts for release 75 are live on www.ensembl.org. You can change your host to access our most recent data: mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path="/biomart/martservice") Ensembl...Genes 75 Renamed Saccharomyces cerevisiae assembly from EF4 to R64-1-1 Added new Transcript source filter and attribute...for all the species …

Saccharomyces cerevisiae Vega Saccharomyces cerevisiae Vega

updated 11.9 years ago • Thomas Maurel

Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287. > entrez_id <- "829795 + 835540 + 832343 + 821775 + 832491...816328 821280 5008021 830796</pre> <pre> > bitr_kegg(entrez_id, fromType='kegg', toType='uniprot', or…

clusterprofiler

updated 8.9 years ago • chentong_biology

Error in EBTest(Data = ebvRna1, Conditions = condition1, sizeFactors = sizes, : Please add gene/isoform names to the data matrix** But I checked my Data by **str(ebvRna1)** **int [1:395, 1:20531] 2 2 2 2 2 2 2 2 2 2 ... - attr(*, "dimnames")=List of...chr [1:20531] "LOC100130426" "UBE2Q2P3" "UBE2Q2P3.1" "LOC149767" ...** It looks I have the gene names for my matrix. Does anyone have …

EBSeq

updated 5.6 years ago • lli2

fit <- lmFit(master_abundance, design_matrix) # Perform statistical testing for differential abundance fit <- eBayes(fit) # Extract fitted values from the fit object using the fitted function fitted_values <- fitted...topTable(fit, coef = "ConditionExperiment", adjust.method = "BH", number = Inf) # Add protein names as a column in master_results protein_names &am…

Proteomics limma

updated 20 months ago • Abbey

at NCBI. I was able to perform DESeq analysis. My questions is with regards to extracting fasta sequences from the original genome based on the results. The results obtained from DESeq use the following gene ID format...gene-NC_027757.2:10030825..10032141 gene-NC_027757.2:10036650..10043774 gene-NC_027757.2:10047118..10049010 gene-NC_027757.2...line): ``` NC_027757.2 Gnomon gene 4576…

DESeq2 Gnomon Biostrings

updated 4.8 years ago • sieminsk

Hello, I am trying to convert ensembl ids to gene names or gene symbol before analysis. How I will convert this? And how I convert in the results file from DESeq2 or EdgerR

ensemblid

updated 6.1 years ago • rajeshparmar4

div class="preformatted">Dear List, I have two sequences of transcripts (they are isoforms from one gene). I would like to align affymetrix's exon sequences and probe sequences

Alignment probe Alignment probe

updated 16.8 years ago • shirley zhang

of newly synthesized to pre-existing metabolite pool. we are assuming this ratio is a ratio between Natural isotopic abundance corrected (M1 + M2 +...Mn) and M0. Mn refers to the last detected isotopic peak provided in the measurement

IsoCorrectoR

updated 5.1 years ago • ffarheen

682397` [1] "IPR019956" "IPR019954" and feeding that into retrain(), I now have the 4th model (most complete?), built using genes: 5667 of 5667 features: 4007 level detectors: 78 This obsoletes my Questions 3 and 4 from my previous...retrain()-generated models I now have, which one is theoretically better to use? The one with the most genes, most level detectors, or most features (domains)? Or …

Genetics Coverage biomaRt gene2pathway Genetics Coverage biomaRt gene2pathway

updated 15.4 years ago • Bogdan