this error.
Error in read.table(URL, sep = "\t", quote = "\"", fill = TRUE, comment.char = "", :
duplicate 'row.names' are not allowed
My generic code is something like this.
kegga(list(Up=up, Down=down),
species="Hs",
universe
Order by: Relevance
at="" gmail.com="">
> Subject: [BioC] how to use normalizeForPrintorder accounting for
> duplicates when there are spots that are not duplicated
in the array?
> To: "Bioconductor List" <bioconductor at="" stat.math.ethz.ch
updated 18.4 years ago • Gordon Smyth
the package and it returns this error:
Error in data.frame(binary= binvers, source = srcvers, row.names = bins, : duplicate row.names: R.utils
So I try to load the package with ... library(oneChannelGUI) and this returns
updated 10.1 years ago • o.j.james
<div class="preformatted">Paul Geeleher <paulgeeleher at="" gmail.com=""> writes:
> Hey Everyone,
>
> I'm having a problem reading some single channel GenePix data.
>
> I use the following code to read the files:
>
> # define column names
> Cy3 <- "F543 Median"
> Cy3b <- "B543 Mean"
I don't think these are …
on
the right side
So...The experiment design involves 3 kinds of replicates: within
array replicate (duplicate spots), technical replicates (as dye swap),
and biological replicates.
I know that at the moment it is not possible...limma to treat this
kind of experiment, but I have an idea how to avoid duplicate spots
(within array replicates), if that is possible.
Here I need your help.
There are…
updated 15.8 years ago • Staninska, Ana, Dr.
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 = HitCount, colData = myCondition, :
ncol(countData) == nrow(colData) is not TRUE
```
In addition, if I run the following code I get this warning:
```
all(colnames(HitCount) == myCondition$SampleID)
[1]…
updated 18 months ago • ussarizona
the p-values listed in toptable were
all
different, the adjusted p-values (adjust="BH") contained duplicate
values.
I don't think this is incorrect necessarily, but I was wondering why
a
different alpha wasn't generated for
updated 14.1 years ago • David Young
see which cell line expresses higher level of what genes.
The problem is, I did not do any duplicates, so I only have one sample per each cell line, and when I tried doing `dds1 <- DESeq(dds1)` it tells me:
The design matrix
updated 3.2 years ago • Jiayi
timepoints sequenced by 10x and would like to compare them against each other. They are all in duplicates (two biological replicates for each TP).
How would one go ahead with duplicated?
Do I need to merge the two biological
updated 5.1 years ago • Assa Yeroslaviz
<div class="preformatted">Hello !
I am comparing the transcriptome of two yeast strains, A and B. For
each
strain we have 5 biological replicates.
The strains are compared to a reference on two-color arrays. For each
biological replicate, we used two slides, in dye-swap.
So we have 20 slides :
slide Cy3 Cy5
1 A1 ref
2 ref A1
3 A2 ref
4 ref …
genes<-readGAL('fish.gal')
> RG$printer<-getLayout(RG$genes)
> maQualityPlots(RG)
Error: duplicate switch defaults: 'list(dev =...' and ''
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)
locale
updated 14.4 years ago • Fabio Liberante
Hi everyone:
I have set of compressedList in the multiple list where each compressedList are corresponds to overlap position index of one set of genomic interval to another, and the order of compressedList in each list are very different. However, I am trying to integrate these multiple compressedList into one without duplication. To make things clarify, this data are the result of finding ov…
updated 9.0 years ago • jian_liangli
next to
each other.
Do you know a solution?
Also another question:
IF one day I manage to do the duplicate correlation and given that I
would
use weights to identfy features with the flag "bad", how will the
software
handle
Running PureCN.R v 1.13.21, I get this warning and these "null device" messages. Are they something to be concerned about?
```
...snip...
INFO [2019-04-29 15:42:06] Fitting variants for purity 0.37, tumor ploidy 3.73 and contamination 0.01.
Warning message:
In .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
INFO [2019-04-29 15:42:06] Fitting…
updated 6.5 years ago • twtoal
Hi,
When converting a GInteractions object into a dataframe, a ‘duplicate row.names’ error is generated.
This is presumably a problem with the as.data.frame function, which encounters...gt; as.data.frame(GInt)
Error in data.frame(seqnames = as.factor(seqnames(x)), start = start(x), :
duplicate row.names: name_1, name_2, name_3, name_4
> GInt <- GInteractions(unname(Gran…
updated 4.3 years ago • noa
me
" There are samples duplicated. We will not be able to prepare it"
How do I get rid of the duplicate files?
My code and session
```
> library(TCGAbiolinks)
> library(xlsx)
> library(DT)
> library(edgeR)
> library(org.Hs.eg.db
updated 4.0 years ago • raf4
on core_mps... OK
Saving DataFrame object for PM.
Saving NetAffx Annotation... Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique...value when setting 'row.names': ‘’
</pre
updated 9.1 years ago • Ed D
and geo\_accession fields moreover that I faced also critical obstacle with duplicated “row.names” , could any one directive me how I can overcome to that essentially dogma, please.
Thank so much for any one will suggest
updated 8.0 years ago • Mustafa ABUELQUMSAN
fit2$t[,2], index=indices[["GO:0001780"]] )
Error in `.rowNamesDF<-`(x, value = value) :
duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names': ‘100506380’, ‘143872...84631’, ‘8553’ </pre>
How can i fix this issue ? i should remove prior the mroast function these duplicates ?
Thank you in advance,
Efstathios
updated 7.1 years ago • svlachavas
limma user's guide 9.6
targets <- readTargets("AllTimePointFiles.csv",path=datadir,sep=",",row.names="filename")
data <- ReadAffy(celfile.path=datadir)
eset <- affy::rma(data)
X <- ns(targets$TimeType,df=2) \# the
updated 8.6 years ago • tjest
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…
expressed genes between a wild-type (Ctl) and mutant (Mut). The mutant has a large DNA duplication encompassing several hundred genes, so they always come up as ~2x upregulated but this is not biologically interesting...tt_2 <- run_cf_eb(H0 = 2, fit) ## H0 is 'ctl = 2 x mut' ##
tt_all <- merge(tt_1, tt_2, by = 'row.names', suffixes = c('.H0_1','.H0_2'))
## Plot logFC from H0('ct…
updated 9.8 years ago • stuart
Annotated” in package ‘IRanges’ seems equivalent to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “DataFrame” in package ‘IRanges’ seems equivalent...to one from package ‘S4Vectors’: not turning on duplicate class definitions for this class.
Note: the specification for class “DataTable” in package ‘IRanges’ seems e…
updated 10.3 years ago • alok.jaiswal
1\]
rownames(countdata1)<-countdata1\[, 1\]
I get the following error: duplicate 'row.names' are not allowed
I have tried so many ways of trying to get this to work, trying solutions other people have
I keep getting from DESeqDataSetFromMatrix function is "Error in `.rowNamesDF<-`(x, value = value) : duplicate 'row.names' are not allowed." I appreciate any advice you can provide.
Code should be placed in three backticks as shown...design=~sex, tidy = TRUE)
# The error I get is:
Error in `.rowNamesDF<-`(x, value = value) :
duplicate 'row.names' are not allowed
In addit…
updated 3.6 years ago • Kevin
carrying out separate channel analysis of two-color data in
limma.
I find that I can not merge the duplicate spots on the arrays. The
function lmscFit() does not provide an argument "ndups" to deal
with the duplicate spots on...the arrays as lmFit() does. Therefore
there
are many duplicate spots in the DE genes. I wonder whether there is a
way to merge the duplicate spots.
Thanks
Dejian
<…
updated 16.9 years ago • De-Jian ZHAO
Hello,
I have been trying to use makeTranscriptDbFromGFF() to read my gff file but I get the following error:
extracting transcript information
Error in .prepareGFF3TXS(data, useGenesAsTranscripts) :
Unexpected transcript duplicates
In addition: Warning message:
In .local(con, format, text, ...) :
gff-version directive indicates version is  …
updated 10.7 years ago • Miss Agnieszka Aleksandra Golicz
Dear List,
I am trying to duplicate the analysis using csaw in the paper, "From reads to regions", https://pubmed.ncbi.nlm.nih.gov/26834993/
I received...out <- suppressWarnings(sortBam(bam, "h3k9ac_temp"))
file.rename(out, bam)
}
# Mark duplicates
temp.bam <- "h3k9ac_temp.bam"
temp.file <- "h3k9ac_metric.txt"
temp.dir <- "h3k9ac_working"
dir.create(temp.dir
updated 4.5 years ago • richardallenfriedmanbrooklyn
I conducted differential expression analysis using limma over several datasets separatly. Now I have several dataframes containing the differential expression analysis for those datasets, and I want to show them on a volcano plot using the MetaVolcanoR package.
If it matters, each dataframe contains a different number of genes. All of them together have about 1900 genes, with 322 duplicate genes…
updated 3.3 years ago • JAcky
other.
>Do you know a solution?
>
>Also another question:
>IF one day I manage to do the duplicate correlation and given that I
would
>use weights to identfy features with the flag "bad", how will the
software
>
<div class="preformatted">Dear Paul,
While I know what this error is, I haven't seen it arise previously in
duplicateCorrelation() with microarray data, so it is hard to give
advice.
It is a numeric error in the inner optimization routine which may
arise
for reasons which are hard to pin down.
Try removing rows from the hx object, e.g., run duplicateCorrelation()
on
the top half or bottom…
updated 16.2 years ago • Gordon Smyth
error density.default(newX[, i], ...) :
'x' contains missing values
Warning message:
duplicate row.names
12,15,20,21,22,25,26,27,31,32,33,34,38,39,40,43,44,45,48,49,50,54,55,5
9,60,64,65,69,70,73,74,75,78,79,83,84,88,89,90,94,95,96...480,483,486,490,491,493,495,498,501,504,506,507,509,510,512,513,5
[... truncated] in: data.row.names(row.names, rowsi, i)
How can I do for next step to de…
updated 17.2 years ago • Yisong Zhen
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...DESeq2. My problem is that for the original sample, fibroblast, they only provide 1 sample without duplicates. I understand that fibroblast is quite general c…
div class="preformatted">I have a data set which pretty much duplicates the experimental design
of one of the limma examples, so I am using that with great results
:-D
There is one difference...though - the limma example has no duplicate
spots, whereas my design does. So I did two runs of limma, one to
find
differentially expressed spots, the other to...differentially
expressed genes (I assu…
control probes using package illuminaHumanv4.db Version:1.26.0
Error in value[[3L]](cond) : duplicate row.names: 200647550006
AnnotatedDataFrame 'initialize' could not update varMetadata:
perhaps pData and varMetadata
rtracklayer??? seems equivalent to one from package
???BiocGenerics??? and is not turning on duplicate class definitions
for this class
Warning in .simpleDuplicateClass(def, prev) :
A specification for S3 class ???terminal...rtracklayer??? seems equivalent to one from package
???BiocGenerics??? and is not turning on duplicate class definitions
for this class
Warning in .simpleDuplicateClass(def, …
updated 12.7 years ago • Guest User
fish.gal')
> > RG$printer<-getLayout(RG$genes)
> > maQualityPlots(RG)
> Error: duplicate switch defaults: 'list(dev =...' and ''
> > sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i386-pc-mingw32/i386 (32
updated 14.1 years ago • Ignacio Lopez De Ullibarri Galparsoro
I wonder that whether the input bam file need to be the raw bam files which include the chrM, duplicates.
When I tried to input the bam file (q30) which was removed the adapters,duplicates, chrM, the fragment distribution...lt; 100bp (which was considered as nucleosome free region) was similar with around 200bp.
The duplication rate is 34%, the %chrM of filtered bam is 50%.
Thank you in …
In the csaw workflow and vignette, it is mentioned that duplicate removal is not always advisable. I couldn't quite understand why that would be. Shouldn't duplicate removal help
SNP), dendrogram construction and estimating the error rate between replicated samples (duplicates/triplicates).
My code :
mat <- 1-ibsmat
mat1 <- mat[-99:-100,-99:-100]
#ERROR RATE FOR triplicates
x <- seq(1,274,3)
err.r <- rep...ibx[lower.tri(ibx)])
}
errorrate <- mean(na.omit(err.r))
#ERROR RATE FOR…
updated 6.8 years ago • meriam.nef
all samples) and I have the following samples to work with:
0h - No treatment, a single set of duplicate samples collected
2 days - duplicates collected for drug treatment and DMSO control
10 days - duplicates collected...for drug treatment and DMSO control
42 days - duplicates collected for drug treatment and DMSO control
My goal with the analysis is two-fold. First, I want to identify …
updated 22 months ago • WS
and I would
like
to have suggestions on the methods I should use to analyse the data.
I have three duplicates done in two different places, so they look
very
different in terms of background and signal intensities. Since...I'm not
going to have more duplicates I would like to get the most information
possible from these, even if I do know that it is not the perfect
experimental...I just compare …
updated 21.7 years ago • Paola Sgado'
48hr
-----------------------------------------------
My previous approach in my analysis was to duplicate the 0hr data
point to
create a control and treatment variation:
-------------------------------------------------
Control 0hr,4hr,8hr,12hr,16hr,20hr,24hr,48hr
vs
Treatment...I am very much a beginner:
>counttable <- read.csv("~/Desktop/Countsdata.csv", header=T,
row.names=1)…
updated 12.8 years ago • Marcelo
Hi,
I was trying to analyze a dataset with a slightly high number of duplicates, (i.e. the duplication rate at the lower end of the expression (reads/kbp) seems to be high at ~ 25%). I am therefore not too
updated 5.7 years ago • Brian Smith
div class="preformatted">Hi-- apologies if this is a duplicate email. I just joined the list
today
and I didn't know how long the email I just sent before I joined would
be
under moderator...just keep GSM
}
}
if(!exists("affyobj")){
mdExprs <- as.matrix(read.csv(defaultExprs,row.names=1))
if( min( mdExprs, na.rm = TRUE ) >= 0 & max( mdExprs, na.rm = TRUE )
>…
object:
library(graph)
g <- graphBAM(data.frame(from="1", to="2", weight=1))
edgeMatrix(g, duplicates=FALSE)
[,1]
from 1
to 2
edgeMatrix(g, duplicates=TRUE) ## here is the problem !!
[,1]
from 1
to 2
edgeMatrix(as(g, "graphNEL"), duplicates
updated 12.3 years ago • Robert Castelo
div class="preformatted">Hello folks,
I'm getting this error when I run duplicate correlation:
corfit <- duplicateCorrelation(mat@hx, design, ndups=3, spacing=1)
Error in glmgam.fit(dx, dy, start = start
updated 16.2 years ago • Paul Geeleher
data
set.
I can calculate the standard deviation using simple function sd( ).
But
there the spot duplicates are not taken into account, only slide
replicates.
After running lmFit(), eBayes() and topTable() the duplicates are
updated 20.8 years ago • Sebastian Thieme
Hello all,
I am sorry for this, but I need to retract my request for help. I am
not
sure LimmaGUI can cope with replicates in the same block (as this gal
file
shows). I was not expecting them to be in the same block and am
getting the
files checked. Sorry to have wasted anyone's time, but I might be back
once
this problem is sorted out...
Thank you and my apologies again,
Liz Brooke-Powell
…
for expressions. I used
the
following commands:
data<-ReadAffy(widget=TRUE) (Read in 2 sets of duplicate arrays, 4
total)
eset<-rma(data)
se.exprs(eset)
A matrix (of the appropriate dim) is returned, but all the entries are...the expresso command (for MAS preprocessing) and
got
the same results.
Any suggestions?
BTW, are duplicate arrays required in order to get standard errors?…
updated 22.5 years ago • Ann Hess
<div class="preformatted">
Hi,
Can anyone help me with the following please?
I have an experiment using two sets of arrays with different layouts
and
therefore different GAL files that I need to analyse together. A
previous suggestion on this mailing list was to normalize and then
combine the log ratios. Can anyone tell me what the code for combining
2
MALists is please?
Secondly one of …
updated 21.5 years ago • Helen Cattan
<div class="preformatted">Hi,
In lmFit(object, correlation), "correlation" is "the inter-duplicate
_or_ inter-technical replicate correlation".
Correlation is calculated using duplicateCorrelation(object, ndups,
block), where "ndups" is the number of spot replicates, and "block"
is used to describe technical replicates.
The help entry for duplicateCorrelation() says that "At this time it…
updated 17.2 years ago • Dries Knapen
ids. Some are ncRNAs on different locations of the chromosome. I am wondering how you deal with duplicates prior to CPM filtering, TMM normalization, and designing the matrix - do you sum or average the read counts per duplicated...gene across all samples or do you remove all instances of duplicates and keep the gene with the highest read count total? What is the best practice
updated 8.9 years ago • es874
do the two class (unpaired) SAM analysis between two groups of
ratios:
group1: C1/C2 and C3/C4 (duplicates)
group2: C5/C6 and C7/C8 (duplicates),
How can I get the ratio of two columns of an AffyBatch file? and how
to make the result
updated 20.7 years ago • Flora Fan
set that came from cytokine membranes.
Each
membrane contains 23 specific cDNA fragments spotted in duplicates.
The
experiment design includes two treatment of interest, stimulant
(pre-activated or non-activated cells) and...on each
membrane, I like to run limma as factorial design. My question is how
I
should handle the duplicate spots (block effect) in limma processing?
Thanks!
JP-
</div
updated 20.4 years ago • Jianping Jin
data.frame", function(from) as.data.frame(from))
as.data.frame.Vector <- function(x, row.names=NULL, optional=FALSE, ...) {
as.data.frame(x, row.names=NULL, optional=optional, ...)
}
setMethod("as.data.frame",
"Vector",
function...x, row.names=NULL, optional=FALSE, ...){
x <- as.vector(x)
a…
I have complete mirdeep2 on my 15 samples. Results included several duplicates but the read counts differed. I have done a lot of research but there is nothing concrete on how to handle duplicates
updated 5.6 years ago • ljbond
Hi everyone,
I am sorry to ask another question, however, there is an error message that keeps me puzzled. When passing over a list of human entrez IDs to reactomePA for GSEA using
<pre>
result <- gsePathway(anaData, nPerm=10000, pvalueCutoff=0.2, pAdjustMethod="BH", verbose=FALSE)</pre>
Rstudio becomes busy and cannot finish computation. When I manually stop it I get the e…
updated 7.4 years ago • martin.busch
preformatted">Dear Bioconductors,
I am working with an array containing 17496 probes spotted in
duplicate. To deal with duplicate spots I used duplicateCorrelation
like this:
cor<-duplicateCorrelation(MA,ndups=2, spacing...but after duplicateCorrelation
the middle one is missing while the two other ones are there in
duplicates. This leaves me clueless...
Any idea?
Best,
Georg
--…
updated 20.7 years ago • Georg Otto
P VALUE META ANALYSIS, are duplicate markers from multiple studies not accepted?
I am conducting a p value based meta analysis with GWAS summary statistics...WARNING: Invalid p-values for 8 other markers also ignored
WARNING: An additional 87 rows with duplicate marker names were ignored
Does METAL not accept same markers from multiple studies with a different p value and
updated 2.9 years ago • Ymberzal
Recent ...
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This should now be resolved
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