Bioconductor Forum

T2_S2_drought (8 columns), performed the comparison and got 23 DEGs. I am wondered that Why the number of the columns uploaded to the Deseq2 affected the number of DEG. Note that the reported DEGs seem to involved in the

deseq2

updated 7.0 years ago • naktang1

<div class="preformatted">Dear all, I am working with microRNA data and as it is very new to me, I have some general questions. I'm hoping that some people on this list who know more about microarray analysis and miRNA than myself might be willing to offer some opinions/advice. First, when doing quality checks on the data, how useful is it to look at the RNA degradation plots with miRNA, …

miRNA Microarray microRNA miRNA Microarray microRNA

updated 12.9 years ago • Fiona

nbsp;3    0.169999731 and i know A=1 , B=2 and C=3 then how i can replace the number with A , B and C???? thank u &nbsp

software error R

updated 9.9 years ago • Angel

Hello, It might be a silly question, but I am struggling with it all day now. Hopefully someone with bright insight may be of any help. I have this df which contains a column with ID names. Some ID names occur one time, other two, and some even 20 times. In other words some IDs are in 1 row, others in many rows. What I would like to make is a new column which numbers the replicate IDs (from 1,…

plyr

updated 10.3 years ago • b.nota

div class="preformatted">I get an error for some chromosomes when running function computeCopynumber(chrom=i, A=A, B=B, calls=genotypes, conf=conf, NP=NP, plate=plate, envir=env...crlmm. The output is: Sufficient statistics . Estimating coefficients . Allele specific copy number . Copy number for nonpolymorphic probes... .Error in crossprod(X[ix, ]) : object 'ix' not found The error origins…

crlmm crlmm

updated 16.7 years ago • Christian Ruckert

1#cstack=sn~StartBioconductorAMI</strong></td> <td>turl~https://s3.amazonaws.com/bioc-cloudformation-templates/start_instance.json”>Start AMI</a></b></td> </tr> </tbody> </table> Alternative links: <ul><li> <table> <tbody> <tr> <td><a target...us-east-1#cstack=sn~StartBiocondu…

bioconductor aws

updated 10.8 years ago • zhihuang

analysis. I have encountered four CpGs whose genomic position exceeds the size of the corresponding chromosome (in base pairs, bp). The positional information is extracted from the annotation of the IlluminaHumanMethylationEPICv2anno.20a1.hg38

EPICv2 EPICv2manifest

updated 9 months ago • Joshua Llano

graph to begin with. what would be cool would be a thick vertical line on the left representing the chromosome and vertical lines to the right showing each probeset's alignment to the chromosome, with each line labeled by

probe graph probe graph

updated 14.6 years ago • Richard Student

graph to begin with. what would be cool would be a thick vertical line on the left representing the chromosome and vertical lines to the right showing each probeset's alignment to the chromosome, with each line labeled by

probe graph probe graph

updated 14.6 years ago • Richard Student

I'm hoping that someone can give some advice a a linkage program that will handle a large number of markers and a reasonably large pedigree. The markers are from the illumina linkage chip , or HT-sequencing. The old...can't handle this problem, even if the pedigree is broken up and marker set reduced to a single chromosome. Thanks in advance Paul [[alternative HTML version deleted]] <…

updated 15.4 years ago • Paul Leo

as opposed to reads not mapping to any of the annotated features.) Is there an easy way to get this number? I was thinking of counting again, this time with inter.feature=FALSE and subtracting the results, but this is not quite...The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. </div

updated 11.7 years ago • Gabriele Schweikert

after approximately 15 minutes. Am I doing something wrong or is there an upper limit for the number of regions in a biomart query? Thanks in advance, Christian > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-pc-linux

biomaRt biomaRt

updated 15.4 years ago • Christian Ruckert

Jaspar TFBS. These tools look very useful! rGADEM provides a list of enriched motifs. The total number of motifs is provided by the nOccurrences function, but I can't find a way to get to know which peak regions do contain...or positions relative to the peak regions) with the same length as nOccurrences, but I only get one number for each motif, with no chromosome associated. Even in the rGADEM …

rGADEM MotIV rGADEM MotIV

updated 14.5 years ago • mattia pelizzola

and "Homo_sapiens.GRCh38.dna.primary_assembly.fa" from Ensembl. They contain information for all the chromosomes. In the `pb_output` folder, I can see that there are reads and hits in every chromsome. However, after the differential...analysis, I can only see events detected in chromosome 1. ```r se_2 <- makeSE(nxtse_path_2) # Assigning annotations to samples colData(se_2)$c…

SpliceWiz

updated 23 months ago • yyu109

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080313/ 5d779344/attachment.pl

updated 17.8 years ago • Weiwei Shi

between two conditions across different cell types in a single-cell dataset. It appears that the number of features (genes) detected changes from one cell type to another, with some cell types having up to 5-6 times more features...events, as p-value correction for multiple testing (both BH or Bonferroni) directly depends on the number of features, thus more genes are likely to end up being signi…

edgeR DESeq2 single-cell scRNAseq zinbwave

updated 4.7 years ago • vincent.croset

doc/ChIPpeakAnno.html) and the package can automatically annotate your peaks and plot a nice bar chart (i.e., how many binding sites map to promoters, 5'UTR, Exons, etc.). However, I can't find any details on how the algorithm decides

chipseq chippeakanno

updated 10.2 years ago • michaelR

I am reading about a new package and I am interested in plotting logo of a protein sequence. The problem is that the author did not specify how one can convert the sequence to number https://www.bioconductor.org/packages/devel/bioc/vignettes/motifStack/inst/doc/motifStack_HTML.html#plot-an-amino...sequence. The problem is that the author did not specify how one can convert the sequence to…

motifStack

updated 6.8 years ago • Bioinformatics

DE test between 10 cells vs another 10 cells, I nearly can't find any DEs. After I increased the number of cells to do DE test ( including above 20 cells), I can get about hundreds of DEGs. So may I ask is there minimum number of

MAST scRNAseq differential expression

updated 6.3 years ago • Andrew_McDavid

batch blast several protein sequences stored in a R data frame, and then filter the results based on homology eg. more than 80%. I can see that there are several packages that seemingly would be applicable, but would most likely

R blast blastsequences protein

updated 8.0 years ago • andres.susrud

How one can display the number of downloads of his/her packages similar to R CRAN on their homepage

DMCHMM Tutorial

updated 6.3 years ago • shokoohi

<div class="preformatted">Hello, I've been using Bioconductor to do the background correction and normalization of my data, but I want to use the probe values themselves instead of a summary value for my statistical analyses. I am able to export the matrix of pm values, but the first column lists the AffyID and probe number together (e.g., 100_g_at1, 100_g_at2, 100_g_at3, etc.). Is there a…

probe probe

updated 22.5 years ago • Jenny Drnevich

gt; exprs.rawData <- exprs(rawData) However, extracting the data itself gives me a different number of rows: > length(pNames) [1] 243982 > dim(exprs.rawData) [1] 292681 6 Ive verified that this result occurs using the sample...http://www.affymetrix.com/Auth/support/downloads/demo_data/mirna_3_sam ple_data.zip Shouldnt the number of probes in the CEL file be the s…

probe PROcess probe PROcess

updated 12.9 years ago • Vicky Fan

consists of two columns of almost 500 K rows (plus 4 lines at the begining that I won't need). The number of rows are the same in every file. I would need to put all these files together, where the first column is common to all...file). Once I have all the columns one after the other I would also need to paste a column with the chromosome number for each SNP (which is in another file, just this i…

SNP SNPchip SNP SNPchip

updated 17.2 years ago • Laura Rodriguez Murillo

preformatted">Hi, The maPalette() function (in the marray package) does not always return the number of colors requested. More specifically, if a middle color is given and the number of colors requested is odd, then maPalette...returns either one more or one less than the requested number of colors: # >>> returns 12 colors <<< maPalette(low="white", …

marray marray

updated 15.6 years ago • Ali Tofigh

these changes. The significant change is a correction to the calcICL function and corresponding bar chart. The core ConsensusClusterPlus function is the same and produces the same results as earlier versions. I recommend

ConsensusClusterPlus ConsensusClusterPlus

updated 14.6 years ago • Matt Wilkerson

RNA-seq dataset. In my top genes, I am getting a lot of genes with no symbol or that do not map to a chromosome and I am not sure if this is normal? I also get mitochondrial DNA-encoded genes ... I feel like something is wrong i.e...annot.inbuilt="mm10", isPairedEnd=TRUE) ``` **2) Created DGE list and added symbols and chromosomes** ``` DGEListGITR <- DGEList(counts=counts$count…

edger

updated 6.5 years ago • melanie.girard

of my research interest, the data I am planning to work on is qPCR data, with much smaller number of genes (from around 30 genes), with relatively big sample size (1000 samples, highly heterogeneous). Apparently...not get scale free topology, and identifying any big module, which I think is because of the small number of genes. I looked up a lot but could not find anyone asking …

WGCNA

updated 8.9 years ago • zson3366

from the above link to see if there is any tool that can convert GO annotations to Enzyme Commission numbers automatically. I went through the file at http:/www.geneontology.org/mapping/ec2go I have a big file which contains...GO Annotations and my objective is to convert those GO Annotations to Enzyme Commission numbers for further analysis. I would like to check if KEGG.db will be able to do …

GO convert GO convert

updated 12.9 years ago • Guest User

<div class="preformatted">Tophat2 cmd: tophat2 -o path/to --transcriptome-index=/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensem bl/NCBIM37/Annotation/Genes/genes /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bo wtie2Index/genome 001.fastq.gz Cufflinks cmd: cufflinks --output-dir path/to --GTF-guide /Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotati…

updated 11.8 years ago • Sindre

of sequencing - In some papers, they mention a "standard score (z-score) of Deseq2 normalized read numbers", if I am right, deseq2 count, and then normalized the count according to sequencing of each replica in order to be able...could be a good numerical value for the comparison...but, how could I get it the normalized read numbers or the Z-score? Thanks Gonzalo

deseq2

updated 6.9 years ago • gonzalo23mj

<div class="preformatted">Hi, I try to analyze MoGene-1_0-st gene arrays. I used the aroma package to do this and came up with an expression matrix, but have no clue, how to assign real gene names to the respective "IDs" (column "item numbers" after aroma normalization and summarization). As a workaround I simply tried to load the mogene10stprobeset.db library and did u<-mget(row.…

Normalization ASSIGN Normalization ASSIGN

updated 15.5 years ago • Maxim

<span style="line-height:1.6">Hi,</span> <span style="line-height:1.6">I'm using </span><span style="line-height:1.6">SomaticSignatures package and i would like to find the best number of signatures that i should use. I could not find </span><span style="line-height:1.6">assessNumberSignatures</span><span style="line-h…

SomaticSignatures

updated 10.5 years ago • Asma rabe

installed, working and accessible from my R terminal: ``` > library('openPrimeR') The number of cores for was set to '2' by 'parallel_setup()'. ---------- system("melting -V") NN_PATH = /usr/local/share/MELTING/Data CLASSPATH = /usr/local...I am able to import primers and templates, and even run a limited set of check_constraints: ``` # load primers primer_obj <- read_pr…

openPrimeR

updated 3.7 years ago • wnussbau

has 4 samples so totally 40 samples. If I am correct n.features should be = 3480 and the n.data (the number of samples that are present in each file) should be = 40. But reading in the file I've got the following error: raw <- readCtData...Ct"]]], ncol = n.data[i]) : data length [5765] is not a sub-multiple or multiple of the number of rows [145] any suggestions? thanks in advance, …

updated 13.3 years ago • alessandro brozzi

Hi Everyone!! I am trying out a Package `Gviz` to make chromosome-wise coverage plot for a genome sequencing experiment. I was planning to plot per-chromosome-multi-sample coverage...lt;- GenomeAxisTrack(t[seqnames(t) == chr]) plotTracks(trackList = c(list(gtrack),dtrack.all), chromosome = chr, from=as.data.frame(t[seqnames(t) == chr])$start, to=as.data…

Gviz

updated 3.5 years ago • rohitsatyam102

div class="preformatted">Hi, Is it normal not to have the same number of sequences in the fastq file and the object generated from readfastq? grep @ SRR062641.filt.fastq | wc -l 187786 &nbsp

updated 12.8 years ago • carol white

is a > package which can map the gene ontology to these IPIs, and plot the > pie chart to demonstrate the molecular function distributions. > > The input is like the following gene IPI IDs: > IPI:IPI00008860.1...Q16204|TREMBL:Q6GSG7|ENSEMBL:ENSP00000263102| REFS > > I want to plot the pie chart of these …

GO biomaRt Category GO biomaRt Category

updated 16.0 years ago • Lavinia Gordon

currently trying to use genomicranges (or any other package) in order to find overlapping regions on chromosomes when matching patients to themselves. In other words, I am trying to find a working way to tell R to delete the patients...who have overlapping start end numbers BUT only comparing the patients to themselves. I need a code in order to do this by matching the patients only to themselves

genomicranges

updated 7.2 years ago • sbailey5

I would like to limit the number of displayed genes (so **not** the categories, which is easily done with showCategory) in the enrichplot heatplot, but have...Function to get my enriched gene sets and then passing that to heatplot. I don't want to limit the number of genes before the gse analysis itself and I also don't want to change the number of the maxGeneSetSize, but would like

heatplot enrichplot

updated 3.0 years ago • Melanie

provides functions to identify minimum common genomic regions of interests based on segmented copy number data from multiple samples. I've found cghMCR package could be very useful for me. The Manual shows how to generate the...segment list using other method. This segment list has the same parameters: 1)the sample id, 2)the chromosome number, 3)the map position of the start of the segment, 4)the…

DNAcopy cghMCR DNAcopy cghMCR

updated 14.3 years ago • viritha kaza

Can anyone please tell me how to retrieve chromosome location for a set of gene id

affymetrix microarrays differential gene expression

updated 8.1 years ago • anandprem1792

<span style="background-color:transparent">I am trying to use ChIPQC to evaluate some horse ChIP-seq data. I am using the following lines of code in a script on a cluster:</span>   _samples = read.csv("Equine\_ChIPQC\_Samplesheet.csv")_ _my\_experiment = ChIPQC(samples, chromosomes=NULL)_ _save(my\_experiment, file="Equine\_ChIPQC\_metrics.Rdata")_   And after …

ChIPQC chip-seq

updated 8.1 years ago • nbkingsley

preformatted">Hi there I am having some issues with my lumi package as I am unable to create the GEO template despite having the lumi library active. Error: could not find function "produceGEOSampleInfoTemplate" Is there

lumi lumi

updated 14.3 years ago • Yu Leng Phua

<div class="preformatted">Dear Pan How are you going? I am having some issues with my lumi package as I am unable to create the GEO template despite having the lumi library active. Error: could not find function "produceGEOSampleInfoTemplate" I would appreciate...How are you going? I am having some issues with my lumi package as I am unable to create the GEO template despite having the lu…

lumi lumi

updated 14.3 years ago • Yu Leng Phua

files. 2 channel array (with reference). Problem is the adjusted file returns an added column of numbers where CLID should be. This column then stops delivering said numbers around line 3154, returning to CLID, shifting

Transcription Genetics Pathways Network Survival Cancer Breast Colon Kidney Leukemia HIV

updated 13.2 years ago • SSc Array Core

there are karyotypic differences between the cell lines. In particular, each cell line has its own chromosome trisomies. I imagine that these trisomies would affect counts in a chromosome-specific manner, and I want to be...running DESeq2, we have a higher number of differential loops on chromosomes that have cell type-specific trisomies. For example, chr3 has a trisomy in one...I know that DESeq…

DESeq2

updated 2.5 years ago • Kathleen Reed

Another point, the gapAllowed is specified " is an integer specifying low threshold of base pair number " is the unit in base pair number, in several examples it seems that the units are in kb??? thanks a lot , code for gapAllowed...mcrs0.25T_5k_2_20M_sdundo.bind1.5 <-cbind ( mcrs0.25T_5k_2_20M_sdundo1.5[, c ( "chromosome", "status", "loc.start", "loc.end","mcr.start", "mcr.end","samples…

DNAcopy cghMCR DNAcopy cghMCR

updated 14.1 years ago • nac

and convenient function to compute on Rle coverages, for instance. However when it is run on several chromosomes and several samples, it can get very memory intensive. For instance on human chromosome 1, it outputs a vector of...length 250 millions, so for several full genomes it is quickly billions of numbers in memory. However, often you don't need a single base resolution. I wanted to suggest…

Cancer IRanges genomes Cancer IRanges genomes

updated 14.7 years ago • Arnaud Amzallag

I’m very interested in using CopywriteR to detect copy number variation in target capture sequencing data. I’m looking to select a tool to implement in a high-throughput bioinformatic...I’m very interested in using CopywriteR to detect copy number variation in target capture sequencing data. I’m looking to select a tool to implement in a high-throughput bioinformatic workflow. Therefore, I won’t …

CopywriteR copy number

updated 9.9 years ago • smcnulty

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lpNet

updated 2.7 years ago • Sonu

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hu6800probe

updated 2.7 years ago • Lil

AA Kredit Loan CusTomer Care Helpline NuMbeR ☎️ 7008172090//9199748209callme helpline number any problem solve

regutools

updated 2.7 years ago • ajit

AA Kredit Loan CusTomer Care Helpline NuMbeR ☎️ 7008172090//9199748209callme helpline number any problem solve

hu6800probe

updated 2.7 years ago • Chulu

300, uniq=TRUE, shift=0, window_size=1000) Reading bam alignment FallBud_brep1_aln_sorted.bam Total number of imported short reads: 21038273 Extending reads... Creating GRange Object... Extract unique regions... Number of unique...reads: 17855868 Calculating genomic coordinates...Error in vector(length = supersize_chr[length(chromosomes)], mode = "character") : vector size cannot be NA/NaN Tha…

Alignment BSgenome BSgenome MEDIPS Alignment BSgenome BSgenome MEDIPS

updated 11.8 years ago • Vining, Kelly

Hi, This is certainly an issue that can be addressed when I submit my package to the tracker (soon-ish), but maybe it can also benefit other developers if I post it here first. I have started writing an extremely basic R Markdown vignette (title page and sessionInfo) in R Studio, starting from the template "Bioconductor PDF Document v.2" in BiocStyle. However, I run into two distinct problems b…

biocstyle

updated 9.5 years ago • kevin.rue

0      1      1  ….. .. ... when i tried finding the best number of signatures  based on RSS and explained variance plots, it was 5 ,when i normalized the counts by the total number...of events observed in each sample, i.e. dividing by the column sums, the best number of signatures became 10, Any idea??   Thank …

somaticsignatures

updated 10.4 years ago • Asma rabe

<div class="preformatted">Dear all, I'm working on a DNA Methylation microarray dataset. The microarray design is "pd.feinberg.hg18.me.hx1". I used the CHARM package to estimate methylation percentile and selected 1000 probes having larger variances of methylation level across samples. The 1000 probe are identified as chromosome coordinate like following. > rnames[1:10] [1] "chr…

Microarray Genetics probe charm Microarray Genetics probe charm

updated 13.5 years ago • Yoo, Seungyeul

Can I pre-set the number of clusters with scater? I'm comparing scRNAseq analysis tools, and the same dataset clustered into 8 by Seurat is clustered

scater scran scrnaseq clustering

updated 7.1 years ago • shbrief

AA Kredit Loan CusTomer Care Helpline NuMbeR ☎️ 7008172090//9199748209callme helpline number any problem solve ✨tc

lpNet

updated 2.7 years ago • Chulu