attribute(s): go_accession, go_namespace_1003
Please use the function 'listAttributes' to get valid attribute names</span></pre>
Thanks a lot.
 
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Invalid attribute(s): go_biological_process_id
Please use the function 'listAttributes' to get valid attribute names
I am thus unable to reproduce previous results.
Have no idea how this could happen, If anyone can help
div class="preformatted">Hello,
Can anyone tell me how to display heatmap with gene names
instead
of Affy probes when displaying heatmap from Affy exprsSet. I looked at
the
heatmap function and exprs class...but I am at a loss as how to change
the
name on the heatmap to Gene name instead of Affy ID.
I managed to get the geneids as follows :
geneid <- mget(geneNames(eset), en…
gives an
error on my machine:
require('rsbml')
com<-new("Compartment",id="default_compartment",name="default_compartm
ent",size=1)
sp<-new("Species",id="s1",name="s1",compartment=com at
id,initialConcentration=10)
re<-new("Reaction...id="r1",name="r1",kineticLaw=new("KineticLaw",math=
as.expression(0)),reactants=list(new("SpeciesReference",species="s1",s
toichiometry...1)))
…
Hello everyone
I have a question related to differential expression analysis at isoform level. I have two samples, control (Ctrl) and knockout (T1). An isoform has been knockout from the sample. Below are the expression
updated 3.9 years ago • Arunima
obtain
your list of probesets of interest. Then potentially looking at
individual probe expression levels across samples for all 11 probes of
that probeset? (but normalized across samples to enable greater
accuracy of the
I am new to array analysis, having started this week, however I cannot find a solution and suspect I must be doing something wrong, so I have resorted to making my first post.
My problem in particular is that I see abnormally...adjusted P-values in topTable, that look so unrealistic that I imagine it must be my mistake. It could be pure coincidence, but aside from the exercise vignettes, of the …
updated 9.9 years ago • Jason
if the reads contain true variation with respect to the original reference sequence. The expression level of a gene could then be cumulative of readcounts across all of its alternate sequences. We are finding it hard...wanted to confirm whether this violates any of the assumptions that DESEq2 makes?
If this sound a valid approach, at what stage should this aggregation be done? …
datasetconfigversion="0.6" requestid="biomaRt" uniquerows="1" virtualschemaname="default"> <dataset name="hsapiens_gene_ensembl"><attribute name="hgnc_symbol"></attribute><attribute name="chromosome_name"></attribute><attribute...name="start_position"></attribute><attribute name="end_position"></attribute><filter name="chromosome_name" v…
Series GSE138260
Agilent-034879 ADchip_1.0 033934 (Probe name version)
In the above GEO Series, I have extracted top genes for differential expression analysis. Some of the IDs are...Series GSE138260
Agilent-034879 ADchip_1.0 033934 (Probe name version)
In the above GEO Series, I have extracted top genes for differential expression analysis. Some of the IDs are as...ACUST_4167_PI426418842
Is…
updated 3.7 years ago • Prateek
nbsp;i would like to ask for some updated questions conserning the appropriate design of multi-level contrasts in limma. In detail, i recently aqcuired some missing phenotype information about my already analyzed-merged...random effect__:
__library(limma)__
__library(statmod)__
__condition <- factor(eset.2$Disease, levels=c("Normal","Cancer"))__
__pairs <- factor(rep(1:30, each …
updated 10.2 years ago • svlachavas
levels in common. (Use
suppressWarnings() to suppress this warning.)
8: In .Seqinfo.mergexy(x, y) :
The 2 combined objects have no sequence...levels in common. (Use
suppressWarnings() to suppress this warning.)</pre>
the result in the first case is an assay like that...3): counts countsLeftFragmentEnd countsRightFragmentEnd
rownames: NULL
rowRanges metadata column nam…
updated 10.4 years ago • dzis
all_colnames, strict.colnames = strict.colnames) :
the DFrame objects to combine must have the same column names
I understand the problem (the column names are not the same in gbm_exp and lgg_exp) but I can't
updated 2.1 years ago • nicolas.tajeddine
can be used in Wordle Unlimited's gameplay. Coming up with a new phrase or changing the difficulty level of a word is a great way to test one's skills or others' skills. For well-informed guesswork, the words on any of the nine lines
updated 21 months ago • minton
affymetrix-provided) annotation package. In the top 100 DEG list, there are many gene names in lower-case letters that I am unable to identify. This includes names such as "shasmar", "tusweyb", "flybler.1" and "nugo". Would
updated 7.9 years ago • Antonio Ahn
div class="preformatted">Hi,
I need some help with the annotation package:
To get the gene name for a given probe I perform something like this:
> zebrafishGENENAME$"Dr.19073.2.S1_a_at"
[1] "annexin A11a"
My question...is: How can I do it the other way around, i.e. get all
probes with gene names containing "annexin"?
Any hint will be highly appreciated.
Cheers,
Georg
</div
updated 19.4 years ago • Georg Otto
run "phyloseq\_to\_deseq2" I get the following error:
invalid class “DESeqDataSet” object: levels of factors in the design have non-unique level names after make.names() is applied. best to only use letters and numbers...for levels of factors in the design
If anyone has any experience with this error or knows what I am doing wrong I'd really appreciate
Please help me to use the function named read.agiMicroRna().
Getting the error given below.
```
> library("AgiMicroRna")
> dd=AgiMicroRna:::read.agiMicroRna(targets.micro
updated 6.0 years ago • topijush
div class="preformatted">Dear list,
can anybody suggest how could I insert gene names in additional to
gene
symbols on my topTable generated by limma with my differentially
expressed
genes?
cheers,
Marcos
Does anybody knows which is the easiest way
and the appropriate package to retrieve some protein names starting
from proteins codes?
Example:
Q7VYR0 -> GTP-binding elongation factor
CAA09473 -> P.69A protein (pertactin
updated 15.8 years ago • Giulio Di Giovanni
nbsp; :
sample.name is not a column in rdata.
I've tried to check all objects containing name, but probably I've missed something!
any suggestion is appreciated
chiara
updated 7.8 years ago • chiara.rigobello
div class="preformatted">Aha! Thanks for the tip - am getting gene names now! And thanks for
the look-see at my script.
Cheers,
Lisa
-A couple of corrections. Background correct is yet doing everything...so the background subtraction has to be
done
-manually. And I now see why you're not getting gene names in your
-toptable. You can use
-
- x <-
- read.maimages(targets,columns=l…
updated 15.3 years ago • Orfe, Lisa
pData$population))
# In my .gpr files all miRNAs contain the string "-miR-" or "-let-" in
their
name
# so the grep function can be used to extract all of these, removing
# all control signals and printing buffers etc.
# You need...check your .gpr files to find which signals you should
extract.
miRs <- c(grep("-miR-", RG$genes$Name), grep("-let-", RG$genes$Name))
RG.final <- RG[miRs…
updated 16.1 years ago • Gordon Smyth
Hello,
I wonder if there is a way to use msaPrettyPrint() with sorted alignement by sequence name without rewriting the output fasta file. I know I can read the output fasta file with python, and re-order the sequences...by the sequence name, but I'm pretty sure there is a quickest way to achieve that.
I mean i want to see in fasta file and pdf file (output from msaPrettyPrint
updated 8.9 years ago • Olorin
I have to make the chromosome name to "4" rather "chr4" because my dataTrack 's chromosome names are numbers without "chr". I read the tutorial, and did the following
updated 10.3 years ago • tangming2005
clinically impactful devices,
procedures, and biomedical informatics resources; test the clinical
validity of those items with likely impact in the personal medicine
clinical enterprise; and to execute high priority projects...field and/or MD, RN, or related advance clinical degree within the
last three years. Candidate must excel at modern bioinformatics
skills such as python, pearl, R, cluste…
updated 12.3 years ago • Doe, Aimee
<div class="preformatted">Dear Bioconductors,
I have a problem defining a contrast using the function makeContrasts
in LIMMA. It seems to me as if my problem has to do with the way the
function deals with groups with names that contain digits and
literals. There was a simmilar question in this mailing list in
January, but as far as I can see it never got answered.
I have a time course exp…
from / citation of how it was redone?
\* I am looking to map the probe IDs to ensembl transcript names, not just the gene names. The package doesn't have this information (only ensembl gene names). Could I obtain this somewhere
updated 10.1 years ago • VSM
Annotation = RangedData(IRanges(start = as.numeric(TSS[, 3]), end =
as.numeric(TSS[,
4]), names = as.character(TSS[, 1])), strand = TSS[,
5], space = as.character(TSS[,
2]))
Best regards,
Julie
On 8/29/12 2:41 PM, "Dingxia Feng" <fengdxia@iastate.edu...start_position, end_position,
strand, description
Please use the function 'listAttributes' to get valid …
updated 13.3 years ago • Julie Zhu
Hi everyone,
Just a small question concerning the visualisation of my gating strategy. I would like to add the gatename to the plotted gates and additionally the statistics.
I used the following script, but I can only get the gate names (names=T, stats=F) or the stats (names=F, stats=T).
#### load flowSet
frames_raw <- lapply(files, full.names=TRUE, alter.names=T, read.F…
updated 9.0 years ago • y.klaver
the relevance of Bioconductor
and the BioC2006 conference to the applicant's research.
Applications must be provided on a single page in PDF or RTF
format with indication of name, e-mail address, scholarship track
(student-contributor...tracks will be contacted to
certify current enrolled status at time of decision.
Applications must be e-mailed to biocworkshop at fhcrc.org.
Applications must …
updated 19.5 years ago • Vincent J. Carey, Jr.
already there (yes, cdf etc.. files can be faked).
thank you very much,
ido
*eg.:
file1:
oligo name, sequence, gene name (for grouping multiple oligos)
file2: annotation
gene or oligo name (if not grouped), annotations....
</div
updated 18.2 years ago • Ido M. Tamir
plasma samples. I am attempting to do rlm normalization with respect to the IgG and anti-IgG levels as is depicted in quite a few publications. The PAA package is very non-descriptive as to how to input the control...TCH gpr files","targets.tch.txt")
tch.control.elist <- tch.elist\[grep("IgG",tch.elist$genes$Name),\]
Note that I checked the indexes of the contr…
updated 10.2 years ago • aaron.kelly
I would appreciate your help with choosing the right structure of result names to answer my research question.
I defined 2 conditions:
1. Strain (WT is the reference level)
2. cell-Fraction (FractionA is...the reference level)
I want to calculate the difference between FractionA and FractionB in N2, then do the same for FractionA and FractionB...MUTANT and next to compare the FractionA-F…
txOut=TRUE, dropInfReps=FALSE, varReduce=FALSE)
problem is the output lost the transcript names, just 1,2,3...for row names.
It was fine when I use the following command, without bootstraps
txi <- tximport(files, type="salmon
Given a very simple DNAStringSet, built like this:
afastafile <- DNAStringSet(c("GCAAATGGG", "CCCGGGTT", "AAAGGGTT", "TTTGGGCC"))
names(afastafile) <- c("ABC1\_1", "ABC2\_1", "ABC3\_1", "ABC1\_2")
I would get a DNAStringSetList where the list elements are grouped by a pattern in the sequence name;
in this example, I would get a list of 3 (ABC\*) elements, with the …
updated 7.1 years ago • s.ghignone
e.g. bmi and age) and a condition that can be both continuous and/or discrete with more than 2 levels (e.g. L1, L2, L3).
**Question 1:** When the condition is discrete and one wants to account for confounding factors then how correct...TreatL2.T2 + TreatL2.T2) / 2,
T1vsAllforL3 = TreatL3.T1 - (TreatL3.T2 + TreatL3.T2) / 2,
levels = design)
fit2 <- contrasts.fit(…
updated 5.7 years ago • kdiamanti
I am wanna to make a matrix \[sample x genes\] from CNV files, level 3, downloaded from TCGA database, but I don't know how can I do that.
Currently I have mapped the segments to genes with help
Hi,
I am trying to draw a heatmap for my 45 topvar gene by the use of heatmap.2, and when I set a `srtRow=45` in my code(below):
heatmap.2( assay(rld)[ topVarGenes, ], srtRow=45, scale="row",trace="none", dendrogram="column",col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
row names collided with each other in messy way.
would you please help me to solve this problem? (a…
updated 4.3 years ago • Elham
was hoping to create a new MRexperiment with a subset of the samples. I would like to use the sample name as the feature for which to select the samples by.
I am able to use the: samplesToKeep = which(pData(obj)$sampleName == "XX...create a new MR experiment. but I can only achieve to get one sample at a time using the sample name, so I go from :
_MRexperiment (storageMode: e…
updated 10.4 years ago • rleonzay
attribute: hgnc_symbol not found, please use the function
'listAttributes' to get valid attribute names
> listAttributes(mart=mart)
<snip>
[8] "adf_swissprot"
[9] "affy_zebrafish"
[10] "affy_zebrafish_primary_db...gt; as well. Part of the error here is produced by an inconistency in
> attribute and filter naming. The attribute for the affyids is
> zebrafish_aff…
Error in DESeqDataSet(se, design = design, ignoreRank) :
all variables in design formula must be columns in colData
I checked my design formula it is like this:
ensgeneID as.factor(colData$condition)
1. ESN0000.... control
I want to have sample names from my summarized experiment (se) in my created DESeqDataSet (dds). I would like to look at the counts data in assay(dds...I want to have sample names from my summarized experiment (se) in my created DESeqDataSet (dds). I would like to look at the counts data in assay(dds) with...sample names rather than the numeric headers that exist:
> assay(dds)
results …
updated 6.8 years ago • shintzen
After posting my first email, I realized that rma and gcrma does the
normailization on probe level and across all the arrays in the group.
But SNOMAD seems working on pair chip comparison only (probe level?
not sure, the...third normalization of SNOMAD should be at probe level
instead of probe set)
I wonder if after the rma I can input the data to SNOMAD to do the
mean normalization and variance…
updated 21.7 years ago • Lizhe Xu
UCSC database.
using the supportedOrganisms() command results in the below error
```Error in names(trackIds) <- sub("^ ", "", nms)```
I have seen previous mentions of this bug having occurred years ago as a consequence of some change...in naming scheme in the UCSC database or something like that, and it was fixed in a later update. Can anyone help me with why I might
updated 21 months ago • thomas
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Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20050901/
c6ab8d9e/attachment.pl</div
updated 20.3 years ago • Groot, Philip de
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updated 19.7 years ago • mark salsburg
fixed, ans.type, auto.reduce.pattern, PACKAGE = "Biostrings")
i think it will call the low level coding.
for example:
trimLRPatterns(Rpattern = Rpattern, subject = subject,
max.Rmismatch=0.1, with.Lindels=TRUE)
subject
is there any package or software designed for
analysis
histone methylation of Arabidopsis at genome level by ChIP-Chip?
any advice will be very appreciated.
Best.
--
Daofeng Li,PhD Candidate
China Agricultural University
[[alternative
updated 16.4 years ago • lidaof
When I use colCustom argument, legendLabels argument does not work and use of expression function in named vector is not supported.
1. Do you know if there is a way to replace the names of keyvals by legend labels in order to be able...black',
'black'))
)
keyvals[is.na(keyvals)] <- 'grey'
names(keyvals)[keyvals == 'dodgerblue'] <- "p-value an…
updated 3.1 years ago • elefth.pavlos
only 2 reps (not with 3) and with hu95 chips with 3 replicates.
The error msg is:
>Error in "names<-.default('*tmp*', value = c("100_g_at", "1000_at",
>"1001_at", : 'names' attribute [12625] must be the same length as the
>vector [12551...probes with
identical
ranks and when the ranks are sorted, some are equal so they drop out,
but
the names vector is still the same…
Hi,
Basically we have a spreadsheet containing all our microarray data, genes in rows and samples in colums. We have 6 batches in total, each containing 5-8 samples (53 samples in total) that were run on 5 different microarrays. I also created a SIF.csv file containing 3 columns : Array, Sample, Batch (See head and tail below). Array goes from 1 to 6, Batch goes from 1 to 6 and sample …
updated 10.6 years ago • kimyoorin1
How to create contrasts which represent comparisons between two factors which are not the reference level (intercept) using a model which contains an interaction term?"
(I do believe the interaction term is the important component...outcome = c(3,2,4,5,3,4,9,8,7,8,8,10,2,3,1,1,3,2,9,9,7,6,8,6))
# Setting levels for fixed effects.
groups$treat <- factor(groups$treat)
groups$time &am…
Hi all,
When retrieving TCGA data using TCGAbiolinks, I am trying to find from where the column names are sourced and how they are decided e.g.
```r
colData(data)$paper_Telomere.Maintenance
```
or
```r
colData(data)$paper_Survival
updated 2.4 years ago • BioInfoBeginnerrr
and three time-points (pre-treatment, after treatment 1, after treatment 2). I want a subject-level baseline to account for subject-to-subject variability.
Thus, my design matrix has three columns: `` dose ``, `` time ``, and `` subject...nbsp; In practice, what I've done is concatenated dose and time into a single factor with levels like `` dose0_time0, dose1_time2 ``; now my design t…
updated 8.7 years ago • glocke01
Hello,
I want to determine if there are genes that are differentially expressed between males and females for each treatment (none, low, and high). For gender my reference level is set as female and for treatment my reference level is set as none. Samples and script below.
<table border="1" cellpadding="1" cellspacing="1" style="width:500px">
<thead>
<tr>
<th scope="col">…
updated 7.3 years ago • fargo
Hello,
I get an HTTP connection error when using `` Gviz::IdeogramTrack() ``:
<pre>
library(Gviz)
IdeogramTrack(genome="hg19", chromosome="chr7")
Error: failed to load HTTP resource
traceback()
18: stop(e)
17: (function (msg, code, domain, line, col, level, filename, class = "XMLError")
{
e = makeXMLError(msg, code, domain, line, col, level, filename,
…
updated 7.8 years ago • enricoferrero
How can I convert entry names such as LYSC_HUMAN into HUGO gene symbols, such as LYZ? UNIPROTKB seems to have another format of identifiers.
```r
head...How can I convert entry names such as LYSC_HUMAN into HUGO gene symbols, such as LYZ? UNIPROTKB seems to have another format of identifiers.
```r
head(keys...Q5TD94" "Q9HA92" "Q9UHA2"
```
These are [accessions][1], whereas I want to c…
updated 4.8 years ago • Dario Strbenac
3084" "23189" "6907" "22866" "55869" "5519" "7314" "471"
so how can i know the full name gene from this R names?
thank you very nutch for any answer
updated 2.7 years ago • chavaleab
div class="preformatted">Hi,
More information about the probe-names problems I'm having with probe
names becoming X12324.at instead of 1234_at
Firstly, this is the version of R I'm using
updated 22.5 years ago • Crispin Miller
Recent ...
Replies
Answer: problem reading bam files into nucleR
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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
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ATpoint
★
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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 …
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efoss
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Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
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Thank you very much! will take that into consideration
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