Hallo,
I am working with DeSeq2 package. When I am trying to create the DeSeq matrix needed for starting the analysis, I get this error:
```
Error in `.rowNamesDF...lt;-`(x, value = value) :duplicate 'row.names' are not allowed
```
even if online I found other posts with this problem, the solutions did not help me.
When...I also get a warning message
```
In addition: Warning messag…
Order by: Relevance
Hi all,
I am having an issue with DESeq2.
One is related to its use in galaxy (did not get an answer on galaxy forum so I thought why not ask here)
and one is related...to the introduction of coldata information in the matrix before running DESeq2 when using featureCounts data.
1) using Galaxy with 2 factors (2 batches/ 2 discinct studies from the litterature), 3 levels...could contribute t…
updated 3.4 years ago • NGS_enthusiast
of question,
I get this:
Error in read.table(file = file, header = header, sep = sep,
quote = quote, :
duplicate 'row.names' are not allowed
when run:
source("http://bioconductor.org/biocLite.R")
on one RHEL 6.3 two other R version
updated 11.1 years ago • Pawel Eljasz
Hello, I'm working with DESeq2 package. When I try to run the code I get this error with the additional warning message:
```
Error in `.rowNamesDF<-`(x, value...value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names': ‘0’, ‘0.0011’, ‘0.0012...data contain gene names as row names and FPKM counts as columns. Here is m…
updated 18 months ago • keremozdel9
I've been trying to follow the DeSeq2 manual (https://bioconductor.org/packages/3.7/bioc/vignettes/DESeq/inst/doc/DESeq.pdf) but I've been hitting a problem...in this part:
> pasillaCountTable = read.table( datafile, header=TRUE, row.names=1 )
> head( pasillaCountTable )
For my data, I have GeneID duplicates and consequently row duplicates. Anyone know
I'm trying to summarize an MSnSet object from PSM-level to peptide-level, and then to protein-level. I do this in two steps because I want to normalize on the peptide level.
However, doing so
<pre>
pepqnt <- combineFeatures(qnt, groupBy = fData(qnt)$sequence, fun = sum)
pepqnt_S <- normalise(pepqnt, "sum")
pepqnt_norm <- normalise(pepqnt_S, "quantiles.robust")
pro…
updated 6.3 years ago • joris.vanhoutven
Hi,
I am trying to get gene list using `` geneList `` function from `` refGenome ``. However, I got the following error.
best,
ilyas.
<pre>
>library("refGenome")
Loading required package: doBy
Loading required package: RSQLite
Loading required package: DBI
> ens <- ensemblGenome()
> cdir <- getwd()
> basedir(ens) <- cdir…
However, I was returned the error message:
Error in `.rowNamesDF<-`(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique value when setting 'row.names': ‘.’
Do you have any
updated 4.2 years ago • lxiao63
Hi,
I'm analyzing label-free proteomics data with DEP, but have run into an error of having duplicate row names.
Here's what I have done:
I have generated unique identifiers as indicated in the DEP tutorial:
```
> head(data...Hi,
I'm analyzing label-free proteomics data with DEP, but have run into an error of having duplicate row names.
Here's what I have done:
I have gen…
updated 3.1 years ago • hele7
Hi. I have used DESeq2 to performed differential analysis.
And now I would like to plot the data using transformed values "rld", but not...Hi. I have used DESeq2 to performed differential analysis.
And now I would like to plot the data using transformed values "rld", but not sure how to determine the means for the biological duplicates. The simplest way I could think of is u…
updated 7.1 years ago • JunLVI
Working with a workflow that uses Fastp -> Salmon -> Deseq2
Is it generally considered good practice to control for Fastp's read duplication rate and/or Salmon's percent mapped...a fair amount of variability across a set of samples in the same prep batch and sequencing run (duplication rate, 22-52%; percent mapped, 82-92%). Duplication rate in particular seems relevant, as I didn…
Hi all,
My data is a data frame of estimated TPM counts, where rows are the genes and columns are the samples.
I'm using "library(biomaRt)" to get ensembl symbols and hgnc symbols.
When trying to change the rownames from enemble to hgnc symbols I get an error which stems from duplicates in hgnc symbols the way I understand it.
The error I get:
> "Error in `.rowNamesDF<-`…
up when an ExpressionSet object is
intended to be created parsing a matrix expression data with duplicate
row names:
> try(myExpressionSet <- new("ExpressionSet", exprs = myexprsunique,
phenoData = myphenoData, annotation...myannotation,
check.names=FALSE))
Error in data.frame(numeric(n), row.names = nms) :
duplicate row.names: blu
I was wondering if there exists a way to crea…
updated 12.6 years ago • nqueralt@clinic.ub.es
counts = Data , group = groups )
At this point, it keeps on giving me this error message:
Error in \`row.names<-.data.frame\`(\`\*tmp\*\`, value = c("ML1,ML32,ML4,ML29,etc", :
duplicate 'row.names' are not allowed
non-unique values...when setting 'row.names':
But I know for sure that my row names are unique! Any advice would be appreciated.…
exprs = myexprs, phenoData =
myphenoData, annotation = myannotation)
Error in data.frame(numeric(n), row.names = nms) :
duplicate row.names: 1368290_at, 1368303_at, 1388202_at
I'd like to fix that in an automated way in order to avoid...the script
abortion. Does anyone know how to detect and eliminate duplicate rows
in an expression matrix in an automated way?
Best regards,
Núria
…
updated 13.2 years ago • nqueralt@clinic.ub.es
Hi,
I have used Salmon to quantify some 126 samples using the mouse ensembl reference cDNA transcriptome. Then I tried to obtained
abundance values using tximport as follows:
<pre>
txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM", ignoreTxVersion = F)
names(txi.salmon)
head(txi.salmon$counts)
###C…
Hi,
I have some RNAseq data from a peer. She only has three conditions - control, shRNA1 and shRNA2; shRNA1 or 2 means two independent experiments to introduce the shRNA to cells, and test for knockdown of genes. Unfortunately, she did not conduct a replicate. I.e., I only have three datasets for DESeq comparison.
I am able to run the Rsubread and categorize in the data.frame:
__design\_shrna=…
updated 6.2 years ago • csijst
Hi,
I am trying to annotate CpG calls ( a methylkit object).
meth_gr has CpG calls coerced into GRanges.
gene_bodies_hg38 has the gene body information extracted from a TXDB object made with Gencode 39 GTF.
I have used the findOverlaps function to find the matches between "gene_bodies_hg38" and "meth_gr" and coerce them into a data frame.
My code is provided sequentially below:
> ma…
updated 2.1 years ago • hasche
An embedded and charset-unspecified text was scrubbed...
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Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060626/
b01995a5/attachment.pl
updated 17.9 years ago • Andre
one for asking it.
I am studying the gene expression of a species that has undergone a duplication event. I have a synteny table of gene duplicates for multiple tissue types, which was derived using the genome...of a related ancestral species (that existed prior to the duplication event).
I want to identify loci where the duplicates have significantly different expressions - I was wonderin…
we've been using DESeq for some of the analysis that we usually perform and now we'd like to jump to DESeq2. We've been checking the DESeq2 manual but it is not clear to us how to switch from one version to the other. Could you please...seems not to be a direct way to translate a step from one to the other, according to the guide of DESeq2.
I am adding below and example of the code that we …
Good afternoon,
A while ago I asked how to treat 3 samples per individual (ID) in a DESEQ2.
It was recommended to use Duplicate Correlation in limma.
I wonder how to combine both packages:
I run my DESEQ2 with...colData,
design = ~ AGE+ DIAGNOSIS + SEX)
I see that the duplicate correlation is run with
dupcor <- duplicateCorrelation(vobj, design, b…
updated 19 months ago • Bine
Hi all,
I successfully ran DESeq2, though I am looking for differential abundance of microbial genera, not gene expression. However, duplicate genera...in my taxa table) are listed out and numbered instead of collapsing. I would like to collapse duplicate genera.
![enter image description here][1]
Here is what I ran to generate my figure:
```deg_plus1 <- transform_sample_coun…
updated 11 months ago • Bretta
I am new to RNAseq and started to analyze my dataset using DESeq2. I first run the `DESeqDataSetFromMatrix` function and found the error message
```
Error in DESeqDataSetFromMatrix...I am new to RNAseq and started to analyze my dataset using DESeq2. I first run the `DESeqDataSetFromMatrix` function and found the error message
```
Error in DESeqDataSetFromMatrix(countData...I am new to RNAseq …
updated 22 days ago • ussarizona
a set of Affymetrix arrays, all of the same type,
among
which there is for each sample a biological duplicate. I was wondering
when I should "group" the duplicates : before normalizing ? After ? I
can't either find how to do it properly
updated 15.1 years ago • ab19@sanger.ac.uk
Dear BioConductor list:
I have a set of one color (cy3) data in which each gene was spotted
duplicate in separate blocks (grids). I looked at how well the
duplicated
genes were correlated by using either "duplicateCorrelation...limma)
or
regular "Pearson" correlation test. Both tests gave out similar values
around 0.55.
Duplicate spots should be highly correlated in intensities. The
correlation…
updated 18.2 years ago • Jianping Jin
Hello Everyone,
I am using DESeq2 for DEG analysis.
I have a total of 8 samples( 1 duplicate for each condition so 4 different conditions)
At this point of
updated 5.1 years ago • Merlin
I have single cell RNA seq data from two groups. When I use DESeq2 to explore differential regulation between the two groups, I visualize them in a plotMA graph. To my surprise this...I have single cell RNA seq data from two groups. When I use DESeq2 to explore differential regulation between the two groups, I visualize them in a plotMA graph. To my surprise this shows...a link to the plot I made…
updated 5.4 years ago • mdroog
Hey Michael
DESeq2 dose not work and I receive this message when I try to run library(DESeq2)
library(DESeq2)
Loading required package: S4Vectors...lt;- data.frame(groups,row.names=colnames(data))
library(DESeq2, quietly=T)
dds <- DESeqDataSetFromMatrix(countData = data, colData = sampleInfo, design...t",quote=F)
I receive this output
> data &…
updated 5.3 years ago • 21464321
I ran DESeq2 analysis( DESeq2\_1.8.2 ) with count data for a chip-seq project(comparing ctrl vs trt with no replicates). All padj...77.7817459305202 1231.78001282697
group10811 97.5807358037436 2000.40508397674</pre>
deseq2 output,
<pre>
group_id baseMean log2FoldChange lfcSE stat pvalue padj
group10810 654.7808793787 <strong> -0.436…
updated 8.3 years ago • keerthisannareddy
Please ignore - I found the problem.
Thanks
Hello,
I have a question on 2 factor design.
I have a design with 2 factors, with duplicates. Here is the design:
<pre>
strain time
strain time
sample1 mut a
sample2 mut b
sample3 wt a
sample4 wt b
sample5 mut a...nbsp;
Hello,
I have a question on …
updated 8.8 years ago • GFM
function, but that
doesn't seem to apply. If I understand correctly, it's for
averaging duplicate spots per probe, not duplicate probes
per gene. It requires the same number of duplicates across
the chip anyway
updated 12.1 years ago • Ed Siefker
I downloaded R 4.1.2 64bit and downloaded DESeq2 in R by
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
Install information...packages/release/bioc/html/DESeq2.html
My code DESeqDataSetFromMatrix use to work in R-3.1.2. with DESeq2 downloded from biocLite.
Now with newer version R and DESeq2, I got the following error. Could anyone h…
updated 2.3 years ago • pam
Hello everyone,
I am using DESeq2 for DEG analysis.
I have a set of experiment which consists of 4 duplicates and
it's not clear how to create the design
time now, I have read the documentation, but I cannot find any information on what is done with PCR duplicates. My question is then also if recount3 removed PCR duplicates (e.g. with picard or some other tool).
Kind regards,
Seline
updated 11 months ago • seline.natalie
of running the following in an R session
install.packages("BiocManager")
BiocManager::install("DESeq2")
library(DESeq2)
countData <- as.matrix(read.csv("count.csv", row.names="id"))
head(countData)
condition <- factor(c(rep...dpd1C",3), rep("NBP",3), rep("dpd1P",3), rep("NBD",3), rep("dpd1D",3)))
coldata <- data.frame(row.names = colnames(countData), condition)
c…
updated 22 months ago • Md. Faridul
Hi everyone I need to run Deseq2, but when I try to run this part of command the following error message appears.
**Error in DESeqDataSet(se, design = design...used
De plus : Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
1 duplicate rownames were renamed by adding numbers**
I am new to R and DESeq2, Please anyone could hepl me to fix this error. Thank
updated 2.6 years ago • Abdou-samad
I am annotating data from a GSE dataset. I want to check that the row.names are equivalent to ID to ensure that there are no mistakes.
<code>gse10072 <- getGEO('gse10072', GSEMATRIX=TRUE)<br/>
g72...lt;- gse10072[[1]]<br/>
total <- pData(featureData(g72))</code>
<code>t1 <- data.frame(row.names(total))<br/>
t2 <- data.frame(…
preformatted">Hi all,
Does anyone know if the shortRead package has functionality to filter
out
duplicate reads, but only reads with more than n duplicates, to avoid
reads
stacks caused by PCR-aplification? I can only find...srduplicated(), but
it
doesn't seem to have functionality for specifiying n duplicate reads.
Thanks in advance!
Regards,
JW,
Uni. of Copenhagen
[[alternative H…
normalisation
mat.vsn <- vsnMatrix(RG.final$R)
#I try to fit a an object by taking into account duplicate spots (2
spots, spacing=1)
fit <- lmFit(mat.vsn, design, ndups=2,
correlation=corfit$consensus,weigth=RG$weights[idx...values from this genes and draw
the heatmap.
The problem is that mat.vsn still contains the duplicate spots, so
extracting the values from the normalized matr…
a statistical question, sorry if it's off topic. I am trying to understand the deviance returned by DESeq2. Could not find an explicit description so I assumed it would be the deviance of the fitted model compared to the saturated...mean expression. To create a reproducible example, I'll work with the pasilla data set as used in DESeq2 user guide. This code from the user guide sets up the DESeq2…
updated 5.3 years ago • Peter Langfelder
So I am no R programmer and my skills in this languages are very limited but I needed to perform a certain analysis in it. I needed to use DESeq2, after many hours I finally got a working script.
library(DESeq2)
a = read.table (file = "superEnhancer_counts.txt",header = T,sep = "\t",row.names = 1)
coldata = read.table(file = "superEnhancer_names.txt",header = T,sep = "\t")[,]
…
class="preformatted">I am looking for references to published papers on microarrays which
mention duplicate spots, i.e., replicate spots on the same array
containing
the same probe. The treatment of the duplicate spots can...be very
brief,
e.g., just to say that log-ratios from duplicate spots were averaged
before
further analysis. I am particularly after papers in mainline
biological
journals
recommended to use the DESeq function to perform differential analysis for it treats the samples as duplicates when calculating dispersion. Does the rlog function do the same thing? Should I use simple log transformation
updated 8.0 years ago • Chao-Jen Wong
Hello I'm having issues generating a Manhattan plot in Deseq2 with the following script . Every time I run the script no Manhattan plot is generated despite using the following...count table
countdata <- read.table("family_revised_RNA-seq.counts_fixed.txt", header=TRUE, row.names=1)
# Remove .bam or .sam from filenames
colnames(countdata) <- gsub("\\.[sb]…
div class="preformatted">
I want to know how to deal with data without replicates using
DESeq2,can you tell me how to deal with it.You can see my codes
below,but it have errors when deal with sample without replicates...output of sessionInfo():
library('DESeq2')
readcount<-read.delim("readcount.xls",row.names=1)
readcount<-round(readcount)
readcount<-r…
updated 10.4 years ago • Guest User
Hello, guys,
I have a problem getting the DEseq2 normalized value. I am using R4.3.2 and DESeq2 version 1.42.0. I have 32 samples for 4 groups. The raw count data is obtained...Hello, guys,
I have a problem getting the DEseq2 normalized value. I am using R4.3.2 and DESeq2 version 1.42.0. I have 32 samples for 4 groups. The raw count data is obtained from Hisat2-string tie pipeline.
I would …
updated 3 months ago • 史哲
0200
>From: "Hoen, P.A.C. 't \(HKG\)" <p.a.c._t_hoen at="" lumc.nl="">
>Subject: [BioC] LIMMA: duplicate correlation
>To: <bioconductor at="" stat.math.ethz.ch="">
>
>Dear all,
>I am analysing results from a spotted microarray...with 9,600 features,
>spotted in duplicate.
>When I calculate the duplicate correlation, as follows:
&…
updated 18.6 years ago • Gordon Smyth
div class="preformatted">Hi Everyone,
If I have duplicates in each slide of my experiment, how do I tell
limma
to handle this?
I am using duplicateCorrelation() function, but...all of them,
For instance, if there are overall 15000 spots in my experiment, and
half of them are
duplicates, Shouldn't I end up just with 7500 genes?
Thank you for your time.
best,
--
Andr?s Pinz?n
http://bioinf.i…
updated 15.1 years ago • Andres Pinzon
I keep getting different errors all of a sudden and I don't know why
I've been getting either:
duplicate 'row.names' are not allowed
when I delete row.names I get:
ncol doesn't equal ncount or I get that there are neg values...to who the count values within the matrix belong to, but don't know how to fix it
> library("DESeq2")
>
>
> gene_count_matrix …
updated 4.9 years ago • skamboj
fData(dataSet_final)) <-fData(dataSet_final)$PROBEID</pre>
But I get
<pre>
Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
duplicate 'row.names' are not allowed
Besides: Warning message:
non-unique value when...setting 'row.names': '227320_at'</pre>
My question is,
1. is it normal to have a duplicate probe unremoved after …
updated 6.6 years ago • peirinl
them with annotateInteractions() and checked the interactions with isInteractionType() I got duplicate interactions in the data.frame. For example if a connection between 2 annotated regions are in anchor1 and anchor2
updated 4.0 years ago • dogancan
python script.
My code in R is:
countData <- as.matrix(read.csv("gene_count_matrix.csv"), row.names = "gene_id")
## make the colData
colData <- read.csv("pheno_data.csv", sep=",", row.names=1)
## check if the colnames are included...else is expected with the exception of rownames. In my .csv file, there are gene names, and the DESeq2 manual also has rownames for the outout. …
div class="preformatted">Dear Noah,
Only one level of duplication can be handled using the
duplicateCorrelation() technique. I
suggest that you average over the most highly correlated...duplicate
level, which is the
side-by-side, then use duplicateCorrelation() for the top and bottom
half. E.g.,
MA2 <- avedups(MA,ndups...From: "Noah Cohen" <ncohen at="" cvm.tamu.edu="">
&…
updated 17.6 years ago • Gordon Smyth
I am completely new to using R and DeSeq2 for RNA-seq analysis. My experimental set up is such that I have 3 biological conditions and 2 replicates per condition. I used featurescount to count transcript per genomic interval. I then plugged this into the following script:
library(DESeq2)
countdata <- read.table("featurescountmatrix.txt", header=TRUE, ro…
updated 5.5 years ago • a.rex
data. Shall I do pairwise comparision of different time points or do time series analysis sing DESeq2. Here is an example code. Please help me with a code to get normalzed counts as well. Here is an example code I have written...after going through DESeq2 Manual.
library(DESeq2) Time = rep(c("0h", "120h", "240h"), each = 2)
Treat = c(rep("Control", 2), rep("Treat", 4))
nameD <- paste(Tr…
updated 5.9 years ago • dryellaboina
I am using below design for DESeq2 analysis, how I can change below PCA CODE to make PCA based on Treatment and compartment?
dds$group <- as.factor(paste...local')
PCA<-plotPCA(rlddds, intgroup = "Treatment", returnData = TRUE)
write.table(PCA, "DESeq2-pca-table-rld", row.names=TRUE, sep="\t");
pdf("DESeq2-pca-5Family-table-rld.pdf");
plotPCA(rld5Family, i…
updated 4.0 years ago • nabiyogesh
am working on a data that use fibroblast RNA-seq result. Another samples have multiple experimental duplicates for each data point which is nice. Some have 3 or more and some have 2 duplicates. I believe it is still ok to use 2 duplicates...in DESeq2. My problem is that for the original sample, fibroblast, they only provide 1 sample without duplicates. I understand...so I am thinking maybe I can …
div class="preformatted">Hi,
Some of you may have answers for this.
It seems that the duplicate reads are very common in mRNA-seq data.
Duplicate reads are those being mapped to exact the same chromosome
location
updated 13.2 years ago • jason0701
BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
library('DESeq2')
library('RColorBrewer')
countFilePath = './count-1.txt'
countData = read.table(file = countFilePath, header...FALSE, sep = '\t', row.names = 1,stringsAsFactors=FALSE)
##make first row the colname
colnames(countData) <- countData[1,]
countData <- countData...colFilePath …
updated 2.8 years ago • salehe.ghasempur
Recent ...
Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
•
0
That ll be helpful. Thank you.
Comment: Log-cpm values from limma
by
Shaimaa Gamal
•
0
I have performed RUVg correction and extracted W, factors of unwanted variation.
According to limma guide,
> In the limma approach
to RNA…
Comment: DSS CpG coverage threshold
by
j.gilbert
•
0
Might be a bit late for the original poster :') but in case anyone else is wondering, the DSS user guide says:
*Q: Do I need to filter out…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
Segmentation is of the whole genome, I'll write some code for doing this later today.
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
I'll take a look later.
For next time, I've edited your post by enclosing the code in triple backticks (on their own link). This properly …
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