Bioconductor Forum

predictCoding as follows for a small set of variants across the complete genome, resulting in the sequence not found error: <pre> > predictCoding(vcf, txdb_hg19, Hsapiens) Error in .getOneSeqFromBSgenomeMultipleSequences...x, names[i], start[i], : sequence ^1$ not found</pre> Both the naming conventions do match, and my vcf ranges appear in range: <pre> &gt…

variantannotation predict coding locateVariants granges

updated 8.2 years ago • tony j

Dear all, I have a set of elements with the following distribution of lengths: <pre> summary(width(positivelincrnas)) Min. 1st Qu. Median Mean 3rd Qu. Max. 470 4164 9872 18940 20790 152600 </pre> and another...5558 20460 59880 58360 4829000 </pre> I would like to get elements from the second dataset (genes) such that they are of the same le…

granges R sample

updated 10.2 years ago • Dimitris Polychronopoulos

0.1 152 4 augustus_masked-lcl_ScwjSwM_1000-processed-gene-0.3 7 5 augustus_masked-lcl_ScwjSwM_1000-processed-gene-1.13 92 6 augustus_masked-lcl_ScwjSwM_1000-processed-gene...lcl_ScwjSwM_998-processed-gene-1.32 0 snap_masked-lcl_…

htseqcounts edger

updated 8.4 years ago • mictadlo

Dear, May I know the difference between the txi$counts and txi$abundance when the countFromAbundance is set to true(scaledTPM or lengthScaledTPM or dtuScaledTPM)? If set to xxxTPM, the

RNAseq tximport

updated 3.3 years ago • snowmattin

with __R__ package __Biostrings__ function __readDNAStringSet. __I am trying to read protein fasta sequence using this function fasta file http://mendel.imp.ac.at/PhyloDome/fastas.html library("Biostrings") fa=readDNAStringSet...protein.fasta") head(fa,1) width seq …

biostrings fasta protein

updated 9.0 years ago • fastabest

KLD2D function. As far as I can tell, the problem occurs when one sample condition (eg DMSO) has an abundance of zero counts, leading to tied ranks and 0-value bandwidths. Should these genes be filtered out? I am hesitant to do...this since some of these genes have high counts in the treated samples, suggesting that they are affected by treatment. Are there any other options

software error DeMAND

updated 7.0 years ago • Jesse Dabney

1.0 ST arrays (i.e. "HuGene-1_0-st-v1" in the @cdfName slot of the affybatch). I want to output gene symbols with topTable, and I'm trying to follow these instructions using the annotate package: https://stat.ethz.ch/pipermail...data/annotation/ If "probeids" is the ID column from the topTable output, when I try getting to the gene symbols using getSYMBOL(probeids, "hugene10stprobeset.db"), ever…

Annotation cdf probe annotate affy limma biomaRt Annotation cdf probe annotate affy

updated 14.0 years ago • Stephen Turner

here that not sure can be easily addressed by using any bioconductor packages. I have a siRNA sequence with 19 nt, I want to search the guide sequence against human genome to generate the following outputs: 1. Any genes...that are mapped to the sequence with max of for example 5 mis-matches; 2. Genome coordinate of the matches Many Thanks! Steve

searching siRNA sequence human genome GenomicAlignment Biostrings matchPattern

updated 6.0 years ago • stephen66

hello bioconductor community, firstly, to those who did - thanks for developing and maintaining biomaRt - i use it often and its a great resource. recently, i have been using biomaRt to look up human gene symbols from public RNAseq data and map them to human ENSG IDs. however, when i try to look up a list of about 30k symbols, only...i use it often and its a great resource. recently, i h…

biomaRt

updated 3.5 years ago • colantuonicarlo

GO.db ``, according to the vignette and this [post](https://davetang.org/muse/2011/05/20/extract-gene-names-according-to-go-terms/). For example using this category `` GO:0009063 ``. <pre> library(org.Hs.eg.db) library(GO.db...lt;- unique(get(go_id, org.Hs.egGO2ALLEGS)) esids <- unlist(mget(allegs, org.Hs.egENSEMBL)) length(esids) # [1] 118</pre> However the `` …

GOseq ensemblid GO

updated 7.2 years ago • mico

When I convert gene_id from `ENSEMBL` to `SYMBOL` or `ENTREZID` using `org.Mm.eg.db` package, most of the genes failed. So I checked the package `org.Mm.eg.db`: It turns out that, a total of 71927 `ENTREZID` records, but only...ENSEMBL`. ```r library(org.Mm.eg.db) orgdb <- org.Mm.eg.db g1 <- keys(orgdb, "ENSEMBL") length(g1) g2 <- keys(orgdb, "ENTREZID") len…

org.Mm.eg.db

updated 4.7 years ago • Ming Wang

Hello, I'm trying to run tximport from my input salmon, the generated tx2gene file had 1,000+ genes but when I ran tximport I got missing transcripts with only RNAs are readable (all the other genes are missing). I could...not find the reason why the tximport produce such output. How do I make my other genes visible? Thanks ```r library(GenomicFeatures) gff_file <- "tn2-sequence.gff3" fi…

DESeq2 tximport salmon

updated 3.0 years ago • camilia.savitri

div class="preformatted">Dear All, I'm trying to use the previous built (within Biomart)for human genes to get gene location, It seems like Ensembl 44 is the version I should use for NCBI 35/hg17, I did following: ensembl =useMart...archive=TRUE) listDatasets(ensembl) [1] dataset description version <0 rows> (or 0-length row.names) So you could see there is no dataset avai…

updated 14.5 years ago • Yan Jiao

Hi all,     have a general question, one that I would really like some help with if somebody would be able to offer some advice. I am using R to analyse my RNA-seq data, however, I work only from the step where the sequences have been aligned and counts generated to form a counts table with ens IDs, so I am not really clued in about the alignment process.  &…

alignment Fastq fasta

updated 7.2 years ago • A

function fails to relist the alignmentPairs object according to the groups (i.e. under each gene name no compatible reads paired were listed as should be). For the paired-end data, how should I relist the compatible reads...of length 2570: $A3GALT2 GAlignments object with 0 alignments and 0 metadata columns: seqnames strand cigar qwidth start end...strand cigar qwidth start end width nju…

GenomicAlignments pakcage extractList

updated 6.5 years ago • Jiping Wang

I am interested in quantifying the microbial content of an RNAseq experiment in a way that allows for statistically comparing abundances of species between samples. There are a few tools that have been built for this that I am using, but I was curious to hear if anyone has thoughts on using pseudo-alignment (Salmon) and DESeq2 for this. The workflow I've tried is as follows: 1) Map reads to th…

salmon deseq2

updated 7.0 years ago • kballa

<div class="preformatted"> setwd("Desktop") annoT=read.table("annoarray.txt") head(annoT) colnames(annoT)<-c("name","symbol","chr","strand","start","end","name2 ","affy","expr") head(annoT) ordering<-as.matrix(annoT[,"expr"]) head(ordering) Top25Expr<-logical(length=nrow(ordering)) head(Top25Expr) peak=read.table("top7000peaks.csv") head(peak) colnames(pea…

updated 13.4 years ago • Guest User

Genome3="<<REPLACE WITH PATH TO FASTA FILE 3>>") # specify where to create the new sequence database db <- "<<REPLACE WITH PATH TO SEQUENCE DATABASE>>" # load the sequences from the file in a loop for (i in...1 and 2 unlist(DNA[[2]]) # Genomes 1 and 3 unlist(DNA[[3]]) # Genomes 2 and 3</pre> Accessing the sequences of…

decipher

updated 8.0 years ago • Vinicius Henrique da Silva

data from a affy experiment). I have 10 normals and 15 cancer lines. of 180 I have some duplicate gene names (arising from two different probesets for a single gene). I want to calculate the median expression value for these...two identical genes. here I have 6 samples and 2 genes. gids N1 N2 N3 T1 T2 T3 T4 G1 10 12 11 40 46 39 …

Clustering Cancer affy Clustering Cancer affy

updated 17.8 years ago • Srinivas Iyyer

div class="preformatted">Dear All, I just noticed that sequence columns the data frame returned by biomaRt's getSequence function contain the string "Sequence unavailable" in...coding", mart = ggMart); This gives me: coding ensembl_gene_id 1 Sequence unavailable ENSGALG00000017787 The ENSEMBL gene in question is some RNA component of a telomerase [1], which expla…

biomaRt biomaRt

updated 11.6 years ago • Jan T Kim

div class="preformatted">hello list: I am using the package "topGO" to analyse GO enrichment of gene sets: and I following the example of topGO 1.2.1package document ( http://www.bioconductor.org/packages/2.0/bioc/vignettes...lt;- filterfun(f1, f2); eset <- ALL[genefilter(ALL, ff), ]; geneNames <- featureNames(eset); length(geneNames); myInterestedGenes <- samp…

GO topGO GO topGO

updated 17.4 years ago • goodgood

R with read10xCounts(h5file). When I look at the rownames of the sce object (see below), the last 12 gene names are CMO301, CMO302 up to CMO312. These are the 10X genomics CMO tags that are used for tagging cells for cell multiplexing...The CMOs should not be added to the sce object as gene names. I could not find an option in read10xCounts to eliminate these rows (nor were google searches produc…

DropletUtils droplet

updated 2.1 years ago • pcantalupo

I have multiple tissue samples (Ie lung and kidney) and need to normalize across tissues. I have gene to orthogroup maps for each tissue and abundance files from Kallisto for each tissue. I am treating each tissue like a...sample. Because I was aware of the fact that tximport needs to have the abundance files and tx2gene maps in the same order, I combined the abundance files for the tissues. For …

tximport

updated 4.2 years ago • nicolette.sipperly

some unexpected behaviour with the annotation package TxDb.Hsapiens.UCSC.hg38.knownGene: several genes on chr21 are unexpectedly long, very different from their corresponding NCBI entries. These genes are CBS (ENTREZID...MIR8069-1 (102466252) & LOC101928269 (101928269). For example, the package sets the CBS gene locus from 6,444,869 to 43,076,378 (length of 36,631,510, see below), whi…

annotation

updated 5.8 years ago • eric.blanc

ENSG00000136143" description [1,] "Heterogeneous nuclear ribonucleoprotein L (hnRNP L). [Source:Uniprot/SWISSPROT;Acc:P14866]" [2,] "Polypyrimidine tract-binding protein 1 (PTB) (Heterogeneous nuclear ribonucleoprotein...hnRNP I) (57 kDa RNA-binding protein PPTB-1). [Source:Uniprot/SWISSPROT;Acc:P26599]" [3,] "Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl- diphosphate farnesyltransf…

GO probe biomaRt GO probe biomaRt

updated 20.0 years ago • Glynn, Earl

<div class="preformatted">Hi, I've been using the DNAbin class and the dist.dna() function in a package I've been making to get a matrix of hamming distances between DNA sequences in a multiple sequence alignment. I've done this with sequences hundreds of thousands long but want to allow the capability to use sequences from genome data i.e. Mbp long. I know there is a Biostring package in …

Alignment Alignment

updated 12.2 years ago • Benjamin Ward ENV

Hello. I was kindly asking how I can convert "Majority protein IDs" to "Gene names" like so: Majority.protein.IDs A0AV96-2;B7Z8Z7;A0AV96;D6R9D6;D6RBS9 A0AVT1;A0AVT1-2 A1L0T0;M0R026 A1XBS5-5;E5RHK0...Q13887-2;A2TJX0;Q13887 A3KFJ0;O14965;Q5QPD4;A3KFJ1;Q5QPD2 A3KMH1-3;A3KMH1;A3KMH1-2 Gene names RBM47 UBA6 ILVBL FAM92A1 ACO2 RPRD1B AAR2 RBM3…

MassSpectrometryData Proteome Database DEP

updated 4.8 years ago • tpm

gt; library(org.Hs.eg.db) # This works fine > mapIds(org.Hs.eg.db, keys = "Q8NGN2", keytype="UNIPROT", column="ENTREZID") 'select()' returned 1:1 mapping between keys and columns Q8NGN2 "219873" # And this does not work > mapIds...org.Hs.eg.db, keys = "P0DPD7", keytype="UNIPROT", column="ENTREZID") Error in .testForValidKeys(x, keys, keytype, fks) : None of the key…

org.Hs.eg.db

updated 4.8 years ago • Masha

belonging to approximately 6 different cancer subtypes. Essentially, I am hoping to first identify "gene modules" of gene expression corresponding to a specific cancer subtype, or groups of subtypes. (e.g. present only in A and...B cancer, but not in C, D, E or F). Subsequently, I wish to label these modules by gene ontology. (e.g. "T-cell response" module) I tried a non-R program (GenXpress) wh…

Genetics Clustering Cancer goCluster Genetics Clustering Cancer goCluster

updated 21.0 years ago • Min-Han Tan

I am trying to map Transcript ID's of the HuGene-1\_0-st-v1 affy chip to their corresponding Gene Symbols. When I do this I am often getting multiple gene symbols for Transcript ID's.  ex:  8029669 -->&nbsp...CT47B1 /// CT47A12 /// CT47A5 /// CT47A10" What would be the best way to choose one of the gene symbols? Also are there any biocondu…

transcript_id gene symbol

updated 10.4 years ago • Jo

alignResults.ch5.BAM", use.names=TRUE, param=param) qseq <- setNames(mcols(gal)$seq, names(gal)) qual <- setNames(mcols(gal)$qual, names(gal)) qseq_on_ref <- sequenceLayer(qseq, cigar(gal), from="query", to="reference") qual_on_ref...qseq_pos_by_chrom <- splitAsList(start(gr), split_factor) cm_by_chrom <- lapply(names(qseq_pos_by_chrom), …

Rsamtools sequenceLayer

updated 4.5 years ago • mike_flower

Hi everyone! I did differential gene expression analysis on an 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 maybe I am using the wrong annotation files etc? For example ``` Gm4724 NA …

edger

updated 6.5 years ago • melanie.girard

Hello ... I have the following chromosome names in my hg19 reference sequence. <pre> > names(seqlengths(tx_by_gene)) [1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8" [9] "chr9" "chr10...Hello ... I have the foll…

reads

updated 11.3 years ago • marcovth

<div class="preformatted"> Hi all, I'm trying to run an analysis on 24 Affymetrix HGu95v2 chips. I've set up, via merge.AffyBatch, an affybatch object containing all 24 arrays. A1 <- read.affybatch("A1.cel") . . . A24 <- read.affybatch("A24.cel") A <- merge.AffyBatch(A1, A2) A <- merge.AffyBatch(A, A3) . . . A<- merge.AffyBatch(A, A24) I then…

cdf probe cdf probe

updated 21.8 years ago • Horswell, Stuart

Hello, I have a timecourse RNA-seq dataset and I utilized natural splines in DESeq2 to identify differentially expressed genes over time. Based on my understanding, the coefficients...interpretable and the only useful thing would be the pvalue. The conventional way to rank genes for gene set enrichment analysis in fgsea is to multiply sign(log2FC) and -log10(pvalue). However, in my case where …

fgsea GeneSetEnrichment splines RNASeq

updated 10 months ago • GT

enter image description here][1]I have run mothur pipeline for amplicon sequencing data. I get phyloseq object now I want to visualize various plots like an abundance of taxa, and a comparison of taxa...is following. Anyone can modify this code for proper graphics. ``` plot_bar(pseq, x="Sample", y="Abundance", fill=NULL, title=NULL, facet_grid=NULL) ``` [1]: /media/images/e8a1804b-8…

Metagenomics phyloseq ggplot

updated 2.9 years ago • abhisek001

countMatrix, colData = SampleInfo, design = ~ geno_stage) but in result file there is no gene names, could you please suggest how I can resolve it? "","baseMean","log2FoldChange","lfcSE","stat","pvalue","padj" "1",2133.39832753799

deseq2

updated 6.7 years ago • nabiyogesh

affordable real estate option [**real estate agency in lisbon**][1]? Get in touch with one of the most eminent real estate agents in Portugal. Central Lisbon is a licensed real estate agency listing thousands of beautiful...you in finding the perfect property in Lisbon according to your needs. Portugal town is a place with natural and scenic beauty. It possesses the power to let you experience th…

QualityControl

updated 4.4 years ago • centrallisbon0

inst/doc/tximport.html) shows two ways to import results for differential expression analysis at the gene level. The first approach (used with DESeq and edgeR) is to use the estimated counts from your quantification tool of choice...and let (or set) DESeq (or edgeR) use an offset to account for changes in average transcript length per sample. The second way is to just fetch `` countsFr…

tximport edgeR DESeq2

updated 9.6 years ago • Steve Lianoglou

too permissive to measure the reads corresponding to a single nucleosome. For example, if the read length was 100, then this allows a 250 range of starting positions to be counted for each window. The approach that makes the...most sense to me is the following: <pre> window.counts <- windowCounts(sample.table$bampath, ext=147, width=1, spacing=73, param...pre> Specifically, thi…

csaw differential binding analysis bin size

updated 9.7 years ago • Ryan C. Thompson

nullp function to create a data frame containing bias and weighting information a substantial \# of genes have no data - that is, NA in both the bias.data and pwf columns. The number of NAs is substantial (2077 genes, or about 10% of...lengths from it.</pre> Related Questions: (1) Does "NA" in bias.data mean there is no length information for that particular Ensembl...gene? And if so, how …

goseq pwf

updated 10.4 years ago • mjnolte

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 PCA analysis on filtered g…

salmon RUVSeq cqn PCA RNASeq

updated 2.7 years ago • ur.n

Hello, I am trying to import transcript abundances (from kallisto .tsv files) to analyze with DESeq2. My goal is to do a gene-level and a transcript-level analysis of differential...expression. In my kallisto files however, I have several transcripts from unidentified genes which does not allow me to directly compare the gene-level with the transcript-level analysis performed in DESeq2 (since..…

tximport deseq2 kallisto

updated 8.1 years ago • Clara

number which I've coded into the column names: ```R ## Load data ------------------------------------------------------------------------ sce <- DropletUtils::read10xCounts( c(paste0(DATA_DIR, "510_Cer_B2/filtered_feature_bc_matrix"), paste0...rowData(sce)$Symbol ``` However, as demonstrated with `510_PFC` above, three of the samples were sequenced over both…

SingleCell SingleCellExperiment scater

updated 4.9 years ago • camerond

and I wonder if someone could give me a piece of advice. I have multiple gene pairs (approximately 8,256) composed by all possible combinations of 129 genes. For each pair A-B (A different from B) four...of tumors found neither in A nor in B (FF). The data are in the form of 2x2 contingency tables. E.g. Gene 1 Gene 2 TT TF FT FF g1 g2 5 1 1 27 g1 g3 4 1 …

updated 13.6 years ago • Efthimios MOTAKIS

a sanity check of my RNA-Seq experiment is driving me crazy. I want to verify that the GFP reporter gene is expressed in my control samples. This reporter gene, of course, is not present in the mouse reference genome but only...transgenic mice. Therefore, I thought to align the short reads of my RNA-Seq fastq files to the GFP gene sequence to verify its mRNA presence in my samples. I came out w…

updated 12.9 years ago • Ugo Borello

div class="preformatted">Hi all, I'm trying to read in a fasta sequence, extract the "gene sequences" and write these out to a fasta file. I can read the sequences with read.DNAStringSet(), obtain...object with Views(), but I'm having trouble knowing how to obtain the reverse complement sequence for the genes on the "-" strand. I can get them with a reverseComplement() of the XStringViews obj…

updated 16.6 years ago • Cei Abreu-Goodger

for RNAseq data (NB model) and then I fit the model with t.fit, I get : 1 754 influential genes with paramater "step.method = forward" 1 146 influential genes with paramater "step.method = backward" 1 755 influential...genes with paramater "step.method = two.ways.forward" 1 126 influential genes with paramater "step.method = two.ways.backward...My second question is : After …

maSigPro TimeCourse

updated 5.6 years ago • DcL-A

Following my [workflow](https://support.bioconductor.org/p/100222/) and advancing one stye at a time, I would now like to convert a `` GRangesList `` object into a `` data.frame,  ``where each of the score columns (meta data columns) of the different GRanges in the list are seaprate columns in the data frame such as : <pre> >tiles.list GRangesList object of length 3: $15…

genomicranges grangeslist dataframe irangeslist lists

updated 8.3 years ago • Assa Yeroslaviz

Hi, I need to rename the DNA sequences of a phyloseq object with ASV1,2,3 and then attach the taxonomy to each new ASV name, so I could export the renamed sequences...as a fasta file. I did this successfully with a phyloseq object of PacBio sequences generated from DADA2 in R, however, when I used the same code with a phyloseq object of MiSeq sequences generated...from exported files from Qiime2…

Biostrings phyloseq

updated 3.8 years ago • Eman

I am using EdgeR to find DE genes in my data. In order to reduce necessary sequencing depth, I have been enriching my sequencing libraries for 300 genes...genes. I am comparing gene expression between two experimental conditions. I have been getting a list of DE genes using the...consisting of biological replicates) and groups identifies the experimental condition. Of the 300 genes that I am ca…

EdgeR deseq2 RNA differential expression

updated 9.3 years ago • tyssowski

library(mixOmics) library(HTSFilter) #Before starting modify the data you have by keeping only gene name and samples with replicates (chromosomes and gene length are not required) #make csv file called (design.csv) contain...symkey=FALSE) ``` then i used the TopGo package as fellow: ``` #Note before analysis #make sure that sequence names in the gene of interest list is similar to that of the ann…

EdgeR RNAseq Foldchange

updated 4.5 years ago • najib

6): ENSMUSG00000000001 ENSMUSG00000000003 ... ENSMUSG00000000037 ENSMUSG00000000049 rowData names(23): baseMean baseVar ... maxCooks replace colnames: NULL colData names(3): SampleID condition replaceable dds2[is.na(dds2...lt;- getGeneLengthAndGCContent(rownames(countsdds2), "mm10", mode="org.db") head(GC_content) length gc ENSMUSG00000000001 3262 0.4421179 ENSMUSG0…

Normalization R cqn

updated 3.2 years ago • Sally

following two simple tasks: >>>>>> >>>>>> 1. I have a list of genes (with gene names from UCSC such as Foxp3 >>>>>> etc...). How do I filter this list to get genes that have certain GO &gt...GO database" concerns the gene ontology, a structure of terms and >&a…

Transcription Annotation GO GOstats biomaRt topGO GSEABase goseq Transcription Annotation

updated 14.9 years ago • Duke

Hello Folks, I generated quant.sf file with Salmon tool and the next step is to Import the transcripts abundance dataset with tximport. I generated the file.csv using the same annotation file used in salmon, > head(tx2gene) TXNAME...Folks, I generated quant.sf file with Salmon tool and the next step is to Import the transcripts abundance dataset with tx…

salmon tximport

updated 6.8 years ago • Merlin

div class="preformatted">Ken Doing a blast of 500 sequences against a database of 500 sequences is not a big job. you hardly need a script for that. And if you want tabular output...alignment programs) works, you just need to blast the fasta against the blast database of the same sequences. You will get output from blast that includes each sequence blasted against all others, with the obviou…

probe probe

updated 20.9 years ago • Rohit Ghai

on this list, I had settled on using regularized log transformed counts in order to present relative abundance heatmaps/barcharts of my metagenomic data. As this transformation accounts for both differing library sizes...to ignore experimental design) or represent the raw counts. This particular taxa is one of the most abundant in my dataset. As you can see, the rlog transformed counts are much m…

updated 12.0 years ago • Kristina M Fontanez

div class="preformatted">I would need help in obtaining all path lengths between two nodes in a directed graph. Suppose I have the following directed graph (below) called "mygraph": > library...6, 5, 6, NULL) > edgelength <- list(c(0,1), c(0,2), 3, 0, 0, "NA") > > edL=vector("list", length=(length(y))) > names(edL)=y > for(l in 1:(length(y))) …

graph graph

updated 11.0 years ago • Victoria V Plamadeala

RefSeq. I have followed the vignette and FAQ to the best of my knowledge however, since hypothetical genes had no names I opted for their WP accession ID instead. The error that occurs is that the sequence names do in my seq input...do not match my gene names in annotation. From what I understand, the protein sequence file supplied for example GCF_000814805.1_ASM81480v1...RefSeq_grangeslist$GCF_0…

syntenet Bacteria synteny

updated 2.2 years ago • kluongni

purpose :-) But. Once you have normalized counts, how would you rank features according to their abundance "within" the sample? How can you tell feature A is more represented than feature B in the same sample? Can you just use...huge genomic domains (megabases, spotted by chip-seq) that change between conditions (in terms of abundance, position and enrichment). I can describe the differences in t…

Normalization edgeR DESeq Normalization edgeR DESeq

updated 12.6 years ago • Cittaro Davide