2,127 results • Page 1 of 36
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 12.0 years ago • Pawel Eljasz
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 &lt;- combineFeatures(qnt, groupBy = fData(qnt)$sequence, fun = sum) pepqnt_S &lt;- normalise(pepqnt, "sum") pepqnt_norm &lt;- normalise(pepqnt_S, "quantiles.robust") pro…
updated 7.1 years ago • joris.vanhoutven
Hi, I am trying to get gene list using `` geneList `` function from `` refGenome ``. However, I got the following error.&nbsp; best, ilyas. <pre> &gt;library("refGenome") Loading required package: doBy Loading required package: RSQLite Loading required package: DBI &gt; ens &lt;- ensemblGenome() &gt; cdir &lt;- getwd() &gt; basedir(ens) &lt;- cdir…
updated 8.6 years ago • Mehmet Ilyas Cosacak
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 message: non-unique values when setting 'row.names': ‘0’, ‘1’, ‘10’, ‘100’, ‘101’, ‘102’, ‘103’, …
updated 4.7 years ago • corellig
However, I was returned the error message: Error in `.rowNamesDF&lt;-`(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 5.1 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: ``` &gt; 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 3.9 years ago • hele7
this error with the additional warning message: ``` Error in `.rowNamesDF&lt;-`(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...design = ~status, tidy = T) ``` My initial data contained duplicate row names; therefore, I tried to remove them by using make.names. After that…
updated 2.4 years ago • keremozdel9
ve been hitting a problem in this part: &gt; pasillaCountTable = read.table( datafile, header=TRUE, row.names=1 ) &gt; head( pasillaCountTable ) For my data, I have GeneID duplicates and consequently row duplicates. Anyone know
updated 6.9 years ago • anokhi1997
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: &gt; "Error in `.rowNamesDF&lt;-`…
updated 4.6 years ago • Matan G.
up when an ExpressionSet object is intended to be created parsing a matrix expression data with duplicate row names: &gt; try(myExpressionSet &lt;- 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 13.4 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&lt;-.data.frame\`(\`\*tmp\*\`, value = c("ML1,ML32,ML4,ML29,etc",&nbsp; : &nbsp; duplicate 'row.names' are not allowed non-unique values...when setting 'row.names':&nbsp; But I know for sure that my row names are unique!&nbsp; Any advice would be appreciated.…
updated 10.1 years ago • ccheung
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 14.0 years ago • nqueralt@clinic.ub.es
could contribute to the 1h treatment of the first batch/study. also in the first study they have duplicates and in the second they have triplicates. I end up with the folliowing error: "Error in `.rowNamesDF&lt;-`(x, value = value...invalid 'row.names' length Calls: rownames&lt;- ... row.names&lt;- -&gt; row.names&lt;-.data.frame -&gt; .rowNamesDF&lt;-" I tried to…
updated 4.3 years ago • NGS_enthusiast
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 3.0 years ago • hasche
An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060626/ b01995a5/attachment.pl
updated 18.7 years ago • Andre
Working with a workflow that uses Fastp -&gt; Salmon -&gt; Deseq2 Is it generally considered good practice to control for Fastp's read duplication rate and/or Salmon's percent mapped (from meta_info.json) when doing a Deseq DE analysis? I have noticed a fair amount...gt; Salmon -&gt; Deseq2 Is it generally considered good practice to control for Fastp's read duplication rate an…
updated 5.5 years ago • rbutler
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 16.0 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…
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
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 21 months ago • seline.natalie
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 &lt;- getGEO('gse10072', GSEMATRIX=TRUE)<br/> g72...lt;- gse10072[[1]]<br/> total &lt;- pData(featureData(g72))</code> <code>t1 &lt;- data.frame(row.names(total))<br/> t2 &lt;- data.frame(…
updated 10.4 years ago • PyPer
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…
updated 15.2 years ago • Johannes Waage
normalisation mat.vsn &lt;- vsnMatrix(RG.final$R) #I try to fit a an object by taking into account duplicate spots (2 spots, spacing=1) fit &lt;- 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…
updated 14.8 years ago • David
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
updated 21.1 years ago • Gordon Smyth
0200 &gt;From: "Hoen, P.A.C. 't \(HKG\)" <p.a.c._t_hoen at="" lumc.nl=""> &gt;Subject: [BioC] LIMMA: duplicate correlation &gt;To: <bioconductor at="" stat.math.ethz.ch=""> &gt; &gt;Dear all, &gt;I am analysing results from a spotted microarray...with 9,600 features, &gt;spotted in duplicate. &gt;When I calculate the duplicate correlation, as follows: &…
updated 19.5 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 15.9 years ago • Andres Pinzon
fData(dataSet_final)) &lt;-fData(dataSet_final)$PROBEID</pre> But I get&nbsp; <pre> Error in `row.names&lt;-.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,&nbsp; 1. is it normal to have a duplicate probe unremoved after …
updated 7.4 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 4.8 years ago • dogancan
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 &lt;- avedups(MA,ndups...From: "Noah Cohen" <ncohen at="" cvm.tamu.edu=""> &…
updated 18.4 years ago • Gordon Smyth
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 14.1 years ago • jason0701
<div class="preformatted">Hi All I haven't used LIMMA for a while, but I remember that when I did there was a special way to handle duplicate spots. However the layout of the array had to be such that one replicate was printed first for all spots and then the...I haven't used LIMMA for a while, but I remember that when I did there was a special way to handle duplicate spots. However the la…
updated 16.7 years ago • Cecilia McGregor
with readGAlignments, I usually set isDuplicate = FALSE &nbsp;in the scanBamParam argument to remove duplicates. I was just wondering exactly how duplicates are determined--is this based on just chromosome and the start and
updated 8.0 years ago • jfiksel
gt;The duplicated spots have random location, which means that the number of spots between each duplicate is not the same for every gene. This is the summary for the distances: &gt; &gt; Min. 1st Qu. Median Mean 3rd Qu. Max. &gt; 4.00...71.00 86.59 135.00 244.00 &gt; &gt;(Distance here means number of spots between the two duplicates) &gt; &gt;The functio…
updated 20.2 years ago • Jason Skelton
vgsID , "GENE.SYMBOL") #then I got Error in `.rowNamesDF&lt;-`(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': ........ ``` I have use the...duplicate() function to check, but the console return FALSE Does anyone have any idea how to solve this? Thanks
updated 2.1 years ago • jscl1n22
the differential binding analysis of some human histone ChIP-seq samples (bowtie2 mapping to hg19, duplicate marking, MACS2 narrow peak calling, blacklisted regions filtering with bedtools intersect and Anshul Kundaje...with the Y vs H comparison: DiffBind: Error in `.rowNamesDF&lt;-`(x, value = value) : invalid 'row.names' length at the point of my script that I was doing a volcano p…
updated 5.8 years ago • melnuesch
gene The duplicated spots have random location, which means that the number of spots between each duplicate is not the same for every gene. This is the summary for the distances: Min. 1st Qu. Median Mean 3rd Qu. Max. 4.00 32.00 71.00...86.59 135.00 244.00 (Distance here means number of spots between the two duplicates) The function duplicateCorrelation in limma can be used to…
updated 20.2 years ago • Ingunn Berget
<div class="preformatted">Hi, I'm trying to use DESeq to know the differential expressed genes of my datasets and i'm encountering that DESeq is not recognizing my row.names so i can't create my cds. My .csv input file looks like: transcript_id,C4,CRL_2APR10,CRL_1_15JUL11,CRL_2_15JUL11 comp1000201_c0_seq1,5.00,0.00,0.00,0.00 comp1000297_c0_seq1,7.00,0.00,0.00,0.00 comp100036_c0_seq1,0.00…
updated 11.8 years ago • Alicia R. Pérez-Porro
permu.size=10000, Pe=0.001) I got this error <pre> Error in `.rowNamesDF&lt;-`(x, value = value) : duplicate 'row.names' are not allowed In addition: Warning message: non-unique values when setting 'row.names': 'cg00042263.ENSG00000146556
updated 6.3 years ago • ghafarpour
an excellent job with limmaGUI! My question is a simple one. The arrays I work with tend to have duplicates on each slide. However, they are not adjacent nor equally spaced and so when setting the spacing of the duplicates...which appears to be compulsory) I just make it up. I presume this makes the correlation between duplicates meaningless but that linear model fits are OK. Comments? Cheer…
updated 21.4 years ago • Peter Baker CMIS, Indooroopilly
Hi Rory, I had been previously, not marking duplicates or removing them in my ChIP-Seq datasets, and instead setting the dba.count bRemoveDuplicates to TRUE. Firstly
<div class="preformatted">Dear List, I had posted earlier about my problem but didn't get any response that could help so I am seeking your help again. I have duplicate spots on my nimblegen array that are position randomized so there is no order to their placement. In Limma when we call the duplicateCorrelation() function, it requires that the duplicate spots have some order to them, lik…
updated 15.9 years ago • Vishal Thapar
Hi,&nbsp; csaw allows one to remove PCR duplicates when doing read counting across windows. My question is how is this functionality actually executed. I generally...mark duplicates using Picard Tools or Samblaster and I was of the view that csaw would remove these reads when doing read counting...wondering if csaw calls some other program (or its own method) internally for marking and remo…
updated 8.4 years ago • asif.zubair
software, specifically with the GUI interface and are running into some problems. Our array has duplicate spots in a top to bottom manner. When we try to have Limma calculate a duplicate correlation we get the error message
updated 18.7 years ago • Manish Neupane
TRUE) &gt; testFile &lt;- tempfile() &gt; write.table(KarinaSusc, testFile, quote = FALSE, sep = "\t", row.names + =TRUE, col.names = TRUE) &gt; eSet &lt;- read.exprSet(testFile) &gt; eSet Expression Set (exprSet) with 7150 genes 7 samples...sample: arbitrary numbering 2.) Second &gt; KarinaSusc&lt;-read.table("Ka_Susc.txt",header=TRUE,row.names=1,…
updated 21.4 years ago • Marcelo Luiz de Laia
div class="preformatted">Dear List, I was wondering if there is a tool which can help me remove the duplicate probes based on the location of the probes?. To be precise, I wanted to select the probe which is closest to the 3'UTR
updated 12.1 years ago • hsharm03@students.poly.edu
than spots that are in the upper and lower half of the array for instance. This means that duplicates that are lets say 10 spots apart probably are more correlated than those 200 spots apart, and I am afraid may "disturb...mistakes during the programming (I''m an R beginner), but I have calculated the correlation between duplicate spots in this way for different methods of background correction …
updated 20.2 years ago • Ingunn Berget
I could order the genes and get them next to each other. My question is, how would I incorporate the duplicate correlation aspect when defining the design in limma? Thank you for your reply and help. Yolande [[alternative HTML
updated 16.6 years ago • Yolande Tra
nbsp; We perform our DE analysis with limma+voom packages with clean reads without&nbsp; PCR duplicates removal. for testing how PCR duplicates would affect DE gene and FPKM value, we also map reads with PCR duplicates...DE analysis with the same pipeline. It turns out that most of the DE genes are overlap in both PCR duplicates removal&nbsp;group and without PCR duplicates removal&…
updated 8.8 years ago • panying0713
I realize some areas may map to multiple locations in the genome, but I would like to eliminate duplicates if possible. For example, I have some DMPs that have multiple "hg19_genes_introns" entries. This is a single position...so I would like it to only have one entry. If the number of duplicates were the same for each position, this wouldn't be as much of an issue, because the proportions would …
updated 13 months ago • hayleyw
div class="preformatted">Dear all, On my microarray I have some genes for which I have duplicate probes, but not for all. Before I do the stats I would like to average the duplicate probes (e.g. GB10001-RA and GB10006...ideas what would be the most elegant way to average out expression values based on the occurrence of duplicate entries in RG$genes$GeneName? Limma can only average duplicates i…
updated 15.0 years ago • Tom Wenseleers
Hello, I am new here. I have certain numbers of duplicates for each Probe ID (approx. 45000) in one column and its samples data values in others 'n' columns(approx.. 230 columns
updated 3.3 years ago • biomyscience
<div class="preformatted">Hello, There seems to be a problem with read.ilmn() with the new version of limma. When trying to read the control file, there is an error that row names are not unique. x &lt;- read.ilmn(files="probe-profile.txt", ctrlfiles="JAlverdy-JDeF- Dec2-13-ControlProbeData-FinalReport.txt", other.columns="Detection?) Error in `row.names&lt;-.data.frame`(`*tmp*`…
updated 11.1 years ago • Scott Christley
different probenames match the same entrezID which results in an error when I try to assign entrezID row.names : “Error in \`row.names&lt;-.data.frame\`(\`\*tmp\*\`, value = value) : duplicate 'row.names' are not allowed”. topTableOut is output from
updated 7.4 years ago • akleens1
Are `AH52264`, `AH66175` and `AH70594` duplicates, arisen due to automated snapshotting of the same resource at different dates? ah &lt;- AnnotationHub() # all ucsc &lt
updated 5.4 years ago • Aditya
File"\],source="agilent") However, I get the following error: Error in data.frame(FileName = files, row.names = names, stringsAsFactors = FALSE) :&nbsp; &nbsp; duplicate row.names: GSM919399\_0361\_ULS\_252483510001\_S01\_GE2\_105...can I tell if E-GEOD-37442 is single-channel or two-color channel 2) How to resolve the issue of duplicate row.names. They appear to have different desc…
Total number of duplicates in ChIPQC differs from multiqc ? I check all chromosomes not just one... In fact 0 duplicates are found with ChIPQC...How ChiPQC retrieve duplicate ? How can it be explain ?&nbsp; Also&nbsp;RelCC is Inf for one of my sample , what does it mean ? &nbsp
updated 7.8 years ago • ZheFrench
getcolproc(CAGE99d) CAGE99p = procset(CAGE99d, colname[3]) and I got following error:- Error in `row.names&lt;-.data.frame`(`*tmp*`, value = c(6995L, 7017L, 7006L, : duplicate 'row.names' are not allowed In addition: Warning message: non...unique values when setting 'row.names': ‘R:A-MEXP-58:210099’, ‘R:A-MEXP-58:210100’, ‘R:A-MEXP-58:210111’, ‘R:A-MEXP-58:210123’,‘R:A-MEXP- [... truncat…
updated 15.5 years ago • Amit Kumar
tdb/potato/microarray_desc.shtml I found that the pattern for replicated spots is non-trivial, duplicates are within a block, but with the upper-left spots duplicated in the lower right of a block, and lower left spots replicated...3) Do something completely different ? Checking the Archive I found very few references to duplicates which are not "columns" , "rows" or "topbottom". Did I miss som…
updated 19.0 years ago • Steffen Neumann
Hi : I have list of `` GRanges `` that needed to apply very specific duplicate removal . I have reason for using specific conditional duplicate removal for my data. However, duplicate removal...condition for each individual `` GRanges `` is different. I want to do complete duplicate removal for first list element; for second list element, I need to search the row that appear more than twice (fre…
updated 8.2 years ago • Jurat Shahidin
Hello everyone, I've encountered an issue with the EPIC v2 manifest where I found roughly 12,256 duplicate CpG entries in the column labeled "Name." For instance, cg00002033 appears as a duplicate. However, when examining...literature search, I was unable to find any previous discussions or solutions to this problem. This duplication presents challenges in identifying differentially methylated…
2,127 results • Page 1 of 36
Traffic: 674 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6