<div class="preformatted">Hi everyone,
Is there a way to retrieve the level for a GO category in R?
As of now I am retrieving terms by using the following code:
> BP_terms <- stack(lapply(mget(GO_BP_Cats_5_more_genes$category,
GOTERM, ifnotfound=NA), Term))
Now I wanted go get the level (3,4,5...,9).
I looked into the "annotate" package and the " .db" (I am using
org.Bt.e…
Order by: Relevance
and 2 samples.]
<< Prepare Data Over. >>
Error in cmdscale(d) : 'k' must be in {1, 2, .. n - 1}
The complete code is as follows：
pd10 <- data.frame(stringsAsFactors = FALSE,
Sample_Name = c("GSM1669564","GSM1669589
updated 3.1 years ago • shuangshuang
dds) >= 10) >= smallestGroupSize
dds<- dds[keep,]
dds
#now 26,392 genes
```
Reference Level:
I was told 10-15k genes for RNA sequencing data is best...so I still have a lot of genes....DESeq2 will also perform internal...results. Is this the best practice for this package?
My next question is, for the reference level. I don't have a normal vs diseased, or control vs trea…
updated 20 months ago • kcarey
<div class="preformatted">
Hello everyone,
I am a statistician at the Ontario Cancer Institute. Recently, I had
to
analyse an affymetrix dataset. The data have been normalized and the
level
expressions were calculated using GC RMA as implemented in R.
My role is to analyse the expression levels (which were calculated
using GC
RMA) using SAM and other statistical techniques.
The expression …
updated 20.5 years ago • Pintilie, Melania
Hello,
Is it ok to plot the values from the LINCS level 4 data ("level4_beta_all_n3026460x12328.gctx")?
I would like to plot the level 4 values for my compound of interest, on
updated 2.5 years ago • Alexandre
try the pipeline of the vignette. The dataset seems to be concatenated from the __individual RNAseq2 level 3 files __which is quite obscure to me. In the vignette the author stated the original dataset has been moved from...There are two compressed files as tar.gz for RNA expression with the second file 130k of size:
* Level 3 Data Archive \[DCC\]:[unc.edu\_SKCM.IlluminaHiSeq\_RNASeqV…
updated 8.0 years ago • yifangt
Hi,
I have a dataset form RNAseq, I have only the ht-seq-counts results. I have 551 patients with cancers that have been sequenced. So I have only one level, one condition. But I have n=551 patients. Can I use Deseq2 to see a differential expression in my patient cohort even if I have no control. Only one level (one condition= cancer) ?
I have use Deseq2 in the past but it …
updated 8.7 years ago • cardin.julie
SR19_AA24_18Aligned.sortedByCoord.out.bam",
isPaired = TRUE, name="S24", col="sandybrown", fill="sandybrown",
cex=0.8)
>for (i in 12:length(targets)){
ID<-targets[i]
start<-genemodel$start[genemodel...feature=="CDS",],
chromosome = chr, start = start, end = end,
Id = ID, feature=ID, group = ID,
…
updated 5.8 years ago • syliang
full.names=TRUE)
Data <- read.celfiles(celFiles)
I got this error:
All the CEL files must be of the same type.
Error: checkChipTypes(filenames, verbose, "affymetrix", TRUE) is not
TRUE
All CEL files are hg-1.1-st-Array
updated 12.1 years ago • Jerry Cholo
when
I type "require(RBGL)" I get the error message that: "Failed with
error: ??'graph' is not a valid installed package?".
I am using R version 2.12.2 (2011-2-25). I am a new user so your
advice would be of great help.
Best wishes
updated 14.6 years ago • joe j
to `` y <- DGEList(counts=rawCountTable, group=group, genes = merged.descriptions) ``
the gene names have replaced by numbers
> logCPM <- cpm(y, prior.count=2, log=TRUE)
> head(y$genes)
gene_name gene_description
3 sp0000003...Root_tip.3
[19] Root_tip.3 Root_tip.3 Leaves.3 Leaves.3 Leaves.3 …
Hello,
I have a question about the validity of using the GLM strategy in edgeR if the design matrix is not symmetric.
I am dealing with RNA-seq data from cultured...Hello,
I have a question about the validity of using the GLM strategy in edgeR if the design matrix is not symmetric.
I am dealing with RNA-seq data from cultured T-cells from mice that are WT or KO'd for my gene of interest. In a…
updated 11.1 years ago • Michael Moore
Hi all!
Using DEseq2 (v 1.30.0) I try to analyze a "complex" data set with 2 factors (A and B) harboring different levels.
Factor A (named hereafter "line") has two levels (infected/non-infected) and factor 2 (named hereafter "group") has 4 (non-infected, mono-infected with 1, mono-infected with 2 and bi-infected with 1 and 2 at the same time).
According to phenotype data, what drives my phe…
updated 4.9 years ago • lessismore
appreciate any suggestions on the following problem : how to
correct
for the changes in the basal level of gene expression, when comparing
2
conditions : let's say :
a gene changes from 100 to 200 in response to hormone (fold change...the experiment (fold change =
1.6)
would need a procedure to correct for the changes in the basal level
(100
to 150) in the experiments for a set of genes. any su…
updated 13.2 years ago • Bogdan
effects**, but **I have an idea for how to do it and would like advice on whether or not it is valid**. By making minor modifications to the gls.series() and lm.series() functions I can extract the AIC values of the fitted...it is certainly possible in practice, but I am not sure whether it is statistically/mathematically valid. One specific concern is that both M1 and M2 show the same value for …
updated 6.4 years ago • c.taylor
div class="preformatted">Hello All,
I am trying to make P/A calls at both probeset and transcript levels
for Mouse gene ST 1.0 array using Oligo.
Here is what I did for probeset level P/A calls
mmNormal_ps <- rma(mmNormal_raw...0.01) > 5)
mm_ps <- mmNormal_ps[ind,]
But I have been unable to implement it at a transcript level, say,
mmNormal <- rma(mmNormal_raw, …
dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data).
2: Named parameters not used in query: internal_chrom_id, chrom, length, is_circular
3: Named parameters not used in query: internal_id...name, type, chrom, strand, start, end
4: Named parameters not used in query: internal_id, name, chrom, strand, start, end
5: Named parameters...not used in query: inte…
updated 8.8 years ago • Leonardo Collado Torres
I'm asking
You for help because i can't find it anywhere.
I want to know how to get an expression level of genes from the .CEL
file.
I've found some information to do it with using a functions like rma
or mas to get an object exprs...from object of class affybatch. But I
need raw expression level before apply any normalization algorithm
(expression directly from cel files). Than I want to save …
updated 20.6 years ago • s_r
However
```
human_txdb
```
failed with
```
TxDb object:
Error: external pointer is not valid
```
As an experiment, I went back to the HPC cluster and changed the R script :
```
human_txdb <- makeTxDbFromGFF(file="human.gff...more explicit error:
```
Error in result_create(conn@ptr, statement) :
external pointer is not valid
Calls:
<anonymous> ... .local -> …
updated 6.2 years ago • O. William McClung
Hi
I'm trying to achieve a Differential Transcript Usage (DTU) analysis, in order to find genes that are differently alternatively spliced between my two conditions.
The package RATs seems to allow this and I saw that two methods were used to find DTU genes:
> At the gene level, RATs compares the set of each gene’s isoform abundances between the two conditions to identify if the …
updated 6.4 years ago • UserAnonyme
limma and was wondering if it's acceptable (Maybe not ideal, but informative). We've been able to validate many of these genes since. I've since read that when using limma with a ComBat modified matrix, the batch covariate
is spread out over 4 arrays.
Hence I think I have a three-fold multiple testing problem,
on gene level, on contrast level (contrasts between conditions) and on
array
level.
If I just apply the same strategy as e.g. method "global
updated 16.2 years ago • Tefina Paloma
Dear Expert(s)
(Sorry if this information is provided elsewhere- i have looked high and low with no success)
I have a RNASeq data set of 22 samples that can be compared to one another in a number of different combinations. Some of the samples are essentially treatment subsets of others. I have used DESeq2 on the countdata ( along with associated colData) to generate both rld…
gt; I am familiar with GenomicRanges & ReadGappedAlignment, but perhaps
at only an intermediate level. I was told this is easy in samtools
(is it the mpileup command?) but cannot find any examples showing how
this might be done...must be a character vector containing the extended CIGAR strings.
### 'at': must be an integer vector containing single nucleotide...hits_at_in_x,
width=1L)
…
updated 12.1 years ago • Hervé Pagès
Hi all,
I can't find the answer with Google, hope an expert here can help. If two conditions don't have hundreds of differential express genes (in some conditions such as peripheral blood Alzheimer vs normal), is it possible with gene set variation analysis (GSVA), can I find pathways behave different between two conditions? ChatGPT4 said changes may be subtle at the gene level but more pronounc…
updated 19 months ago • Chris
Hello,
I am following along with an RNA-Seq Pipeline with ambiguous steps. I was told they quantification was performed like so: "We used subread to summarize counts to the gene level."
These are the parameters that I am using:
```
mock1 <- featureCounts(files="mock1_Aligned.sortedByCoord.out.bam",isPairedEnd=TRUE, GTF.featureType="exon",
GTF.attrType="gene_id", annot.ext= "gencode.v4…
updated 3.0 years ago • Sara
HI!
I've been trying to use RSubread to count alignments for a RNA-seq course. To get the .bam aligned and mapped file I used Trim Galore, STAR and Samtools in conda enviroment using Ubuntu for Windows. With this file I run the following in Rstudio (Windows 10) and get an error refering to an invalid EOF block. The thing is, i've checked this in samtools and every file I am using has a good EOF …
updated 4.1 years ago • v.merino.nicolas
my?RNA-
seq?data,?following?the?instruction?file?"Di
erential?expression?of?RNA-Seq?data?at?the?gene?level?the?DESeq?packag
e"?step?by?step.?It?didn't?show?any?error?information?until?I?typed?th
e?command?"cds?=?estimateDispersions...cds?)".?The?error?message?was:
Error?in?if?(nr?<?2)?stop("nrow(modelMatrix)?must?be?>=2.")?:
??argument?is?of?length?zero
My?input?file?is?attached.?Could?so…
updated 11.4 years ago • 梁芳
Name_RNA", "IBD")], optimal=c("Sample Name_RNA", "IBD"))
## Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column
In this case the data.frame is small, but it also fails with more rows
traceback()
## 11: stop...ngettext(sum(bad), "'by' must specify a uniquely valid column",
## "'by' must specify uniquely valid columns"), domain = NA)
## 10:…
updated 7.4 years ago • Lluís Revilla Sancho
TPM, FPKM, and IsoPct. And for the same gene_id more than two transript_id .. so it's a transcript-level dataset
![dataset][1]
[1]: /media/images/9e326609-2cd7-4e96-a7d5-ff30122a
I thought I need to use tximport to convert it to counts
updated 2.9 years ago • Hicham
I'm trying to analyze bam files using the csaw package. One of the first steps is to provide your the path to individual bam files, as shown in the csaw manual, page 8. Here is a screen cap from the csaw manual illustrating the expected format of the bam.files variable: ![enter image description here][4]
I have created a csv file, "bamdata.csv' using bash. It contains two columns with hea…
updated 6.4 years ago • vanbelj
gt;tmp<-getGEO('GSE3526',GSEMatrix=T)
> tmp2<-combine(tmp[[1]],tmp[[2]])
Error in alleq(levels(x[[nm]]), levels(y[[nm]])) && alleq(x
[sharedRows, :
invalid 'x' type in 'x && y'
Checking to make sure that I should be able to combine...them (from the
eSet documentation):
#eSets must have identical numbers of 'featureNames'
> all(featu…
updated 17.9 years ago • Francois Pepin
which="core+affx", unitID=unlist(id))
Error in .local(object, ...) : only 1 of 2 UNIT_ID are valid
The reason for this error is that only transcript_cluster_id "3326635"
belongs to level "core" while "3326730" belongs...lt;- split(idx[,"UnitName"], idx[,"UNIT_ID"]);
> unitid <- lapply(unlist(id), function(x) names(which(unitid ==
x)));
> unitid
[[1]]
[1] "185195"
[[2]]
[1…
updated 14.3 years ago • Lavorgna Giovanni
Summits on Un0097 ..</span>_
_<span style="background-color:transparent">Error in names(res) <- nms :</span>_
_<span style="background-color:transparent"> 'names' attribute \[20\] must be the same length as the vector...fictitious chromosome called "chromosome unknown" which accounts for the "Un" part of the chromosome name.</span
<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...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...correlated duplicate
level, which is the
s…
updated 19.2 years ago • Gordon Smyth
Dear Christian,
thanks for your answer. Sorry for not being clear in my previous
massage. I'll try to clarify things a little bit more.
The following script running in a R session ( xps_1.12.1 + root
5.27/04) crashes after finishing the rma step, i.e., it completes the
line:
rma.ps.core <- rma(data.mix.exon, "MixExonRMAcorePS_prostate_CPU2",
filedir=libdir, tmpdir="", background="antigenomic…
updated 14.2 years ago • Lavorgna Giovanni
version of Picard I get
<pre>
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 1, Read name K00280:111:HWNMLBBXX:7:1101:1174:14643, Mapped mate should have mate reference name...1174:14713 81</pre>
Anyway, is there some trickeration that needs to be done (other than using VALIDATION\_STRINGENCY=DONTBOTHERMEABOUTFAKESTUFF
updated 7.1 years ago • James W. MacDonald
Dear DESeq2 community,
I am just wondering whether I can use DESeq2 to perform transcript-level differential expression with Salmon quantification data? And if I can, is that essential to include bootstrap when...using Salmon? I saw a tutorial said DESeq2 will not work if one want to do transcript-level differential expression, just curious whether it is true or not.
Thanks
updated 5.3 years ago • Rain Yi
Error in .local(x, i, j = j, ...) : 'i' must be length 1 in using OrganismDbi to create org.XX.eg.db
Hallo!
I am currently writing my masters thesis and am trying to create an org.*XX*.eg.db object for *Pon abelii*, for a GO analysis with the R-package clusterProfiler, and this requires this kind of object. For orangutan this does not exists as an already available R-package. I created a TxDB object and wanted to use the command "makeOrganismDbFromTxDb(txdb_Orang, keytype="GENEID", orgdb=NA)…
updated 5.3 years ago • amafon95
day) samples taken under 3 time point with 2 replicated for each time point. I have a factor with 3 levels
condition
Day1
Day1
Day3
Day3
Day7
Day7
I am trying to get the DEGs between Day3_Vs_Day1, Day7_VsDay1 and Day7_Vs_Day3...directory, design=~condition)
colData(ddsHTSeq)$condition<-factor(colData(ddsHTSeq)$condition, levels=c('Day1','Day3','Day7'))
colData(ddsHTSe…
I am trying to perform DMP with a dataset of 92 observations in 3 levels. When I run champ.DMP I get the following output:
[ Section 1: Check Input Pheno Start ]
You pheno is factor type.
Your pheno...to Compare : Buffy, Polymorphonuclear
Contrast Matrix
Contrasts
Levels pLymphocytes-pBuffy
pBuffy …
updated 6.2 years ago • ognjen011
div class="preformatted">I use the following code to do RMA. I'm wondering how get the probe
level values before the summary to the probeset level values.
library(oligo)
data<-read.celfiles(list.celfiles(data_dir
updated 15.9 years ago • Peng Yu
a variable that can be passed to justRMA (see
?justRMA for the help file). If you want the column names to be the
cel
file names, just do
Data1 <- justRMA ( phenoData=pD1)
exprs2excel(Data1,"spreadsheetname.xls")
You will have...to hand enter 'Gene Names' in the first cell of the
spreadsheet. You could probably hack the code for read.table() to get
it
to put 'Gene Names' in the...all the…
updated 21.7 years ago • James W. MacDonald
Hi
I was trying to do KEGG and GO analysis in R using clusterProfiler.
<pre>
rm(list = ls())
dev.off()
library(clusterProfiler)
library(org.Hs.eg.db)
x <- "ENSG00000183733"
# human figla
x.df <- bitr(x, fromType = "ENSEMBL",
toType = c("ENSEMBL", "ENTREZID", "SYMBOL"),
OrgDb = org.Hs.eg.db)
gene1 <- x.df$ENTREZID
ggo …
updated 7.7 years ago • niranjan.shirgaonkar
ACCN] with Reference Series: GSE2457
I want to `Collapse individual probe intensities to gene-level (EntrezIDs) measurements` but I get this error
> > filt_eset <- featureFilter(eset, require.entrez = TRUE, remove.dupEntrez...Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'PROBEID'. Please use the keys method…
<div class="preformatted">Hi all ,
My data and question can best be related to section 8.7 in the Limma
manual
Multi-level Experiments. However, lets replace Tissue with Time
with the
idea to measure expression changes overtime that are different...Hi all ,
My data and question can best be related to section 8.7 in the Limma
manual
Multi-level Experiments. However, lets replace Tiss…
updated 12.4 years ago • Michael Breen
div class="preformatted">Hi,
When I do Data<-ReadAffy(widget=TRUE), the sample names appeared to be
what I want, i.e. 10E, 2D, etc. But, after the data are read, when I
type sampleNames(Data), the sample names...is the whole path of the
file,
like c:\my documents\....\....CEL, the names are simply too long for
histogram. Anybody know how to fix the sample names?
Th…
updated 21.8 years ago • Yen Lin Chia
later
continuing to try
Getting extra data for P31946, P62258
Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column
updated 5.0 years ago • Apoorva
row.names(eset);
Systematic = as.character(unlist(mget(Probesets, y2systematic, ifnotfound=NA)))
names(Systematic) = Probesets
Common = as.character(unlist(mget(Probesets, y2common, ifnotfound=NA)))
names(Common) = Probesets...nbsp; design = model.matrix(~0 + samples)
colnames(design) = levels(samples)
&n…
updated 10.9 years ago • Thomas.F.Hahn2
T, sep="\t')
note: phenodata.txt is a text file with variables in columns and
samples
number and/or names in rows. The output file appears to have the
correct
number of cases (133) and variables (20)
Then I create a file, x, that has...all the CEL file names.
Then I attempt to create a Affybatch using justRMA:
Data1 <- justRMA (sampleNames=x, phenoData=pD1)
The output file, a matrix.…
or median
tss.avg <- viewMeans(tss.cov)
tss.med <- viewApply(tss.cov, median)
tss.cov has names for each gene feature:
> class(tss.cov)
[1] "SimpleRleViewsList"
attr(,"package")
[1] "IRanges"
> tss.cov[[1]][1:3]
Views on a 230218...20.3 20.1 20.0 19.8 19.1 ...etc.
[3] 166167 166366 200 [14.9 14.9 15.1 15.1 15.1 15.1 ...etc.
> names(tss.cov[[1]])[1:3]
[…
I want to add a column with name "category" to my data, how can i do that?
input:
col1 col2 col3 col4 col5
1 20 + 4 6
2 24 - 6 7
....
output:
col1 col2 col3 col4 col5 col6
1 20
cn\[, 6\], chrom = cn\[, 1\], maploc = cn\[, 2\], data.type = "logratio") :
genomdat must be numeric
But the data in the coloum 6 of "output.copynumber" are all decimal numbers, so I am confused why I got this
Dear Gordon and all,
I'm analyzing Illumina 450K methylation data with following study design:
Study design: I have individuals at a given time-point from three different stages: Stage 1, 2 and 3 and I wish to identify differentially methylated CpGs in these groups. Stage 1 vs Stage 2; Stage 1 vs Stage 3 and Stage 2 vs Stage 3
I have preprocessed my data and adjusted for batch effect…
updated 9.1 years ago • DSP
<div class="preformatted">Dear Jose
As you say, the jpegs are only 8 bit. Also, Matt Ritchie told me the
tiffs
are 80MB and my files are only 880KB. I've talked to the people who
did the
scanning and the tiffs were deleted because they are so big. However,
they
are rescanning them for me, so I should have the tiffs next week.
Thanks for your help.
Krys
-----Original Message-----
From…
Just out of curiosity, are there any plans for transcript level differential expression (I.e. Supporting fractional counts), with DESeq2??
 
updated 10.6 years ago • andrew.j.skelton73
pairwise data I have.
I've populated my hypergraph by creating hyperedges for each of my sample names that meet a pairwise threshold criteria with other sample names. For example: is sample_A shares a pairwise value of...c_chosen], nrow = length(r_chosen), ncol = length(c_cho
>Selection: 2
>Called from: top level
>Browse[1]> ls()
[1] "byrow" "data" …
updated 6.0 years ago • john.horne
The Center for Biomedical Informatics (CBMI), Harvard Medical School has one junior software programming position available for immediate appointment. The position is part of the Laboratory for Personalized Medicine (LPM, lpm.hms.harvard.edu) program in Personalized Medicine whose mission is to identify and translate biomedical informatics methodology, analysis and applications into the clinical …
updated 11.1 years ago • Doe, Aimee
Hi,
I am trying to RMA normalize a bunch of cel files and output the gene
expression matrix to gene level (instead of probe set level), is there
any
option in justRMA that can do this (or any other function that can do
this?) I searched
exprs(esetSel), col = topo.colors(75), scale = "none", :
'ColSideColors' must be a character vector of length ncol(x)
Kindly help me regarding above error during construction of heatmap.
Thanks
 
updated 8.9 years ago • rkp
Recent ...
Replies
Comment: GOseq Probability Weight Function bad fit
by
ejasge.r.m
•
0
When performing GO analysis with GOseq, i s important to carefully check your input and assumptions, just like reviewing choices on the McD…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★
5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴
10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma
by
Gordon Smyth
53k
Answered here: https://support.bioconductor.org/p/16318/
Awards
• All
Commentator to
sina.nassiri
▴
130
Popular Question to
Hervé Pagès
16k
Popular Question to
jared.andrews07
▴
30
Popular Question to
shepherl
4.2k
Locations
• All
Melbourne, Australia, 21 minutes ago
WEHI, Melbourne, Australia, 24 minutes ago
WEHI, Melbourne, Australia, 2 hours ago
United States, 3 hours ago
The city by the bay, 3 hours ago
Melbourne, Australia, 21 minutes ago
WEHI, Melbourne, Australia, 24 minutes ago
WEHI, Melbourne, Australia, 2 hours ago
United States, 3 hours ago
The city by the bay, 3 hours ago
Traffic: 725 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6