User: Steve Taylor

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Steve Taylor100
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11 years, 10 months ago
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13 years, 10 months ago
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s******@molbiol.ox.ac.uk

Posts by Steve Taylor

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Z factor and Z' factor
... Hi, Please can someone explain what is the difference between Z-factor and Z'-factor as reported in cellHTS2? Many Thanks, Steve ...
written 11.9 years ago by Steve Taylor100 • updated 11.9 years ago by ligia@ebi.ac.uk50
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Specifying wells in normalization for cellHTS2
... Hi, I would like to specify normalization based on certain negative control wells using the package cellHTS2. I am trying: xn<-normalizePlates(x,scale="multiplicative",log=FALSE,method="negativ es",varianceAdjust="none",negControls=c("B12","C01","C12","D01","D12", "E01","F01")) but get: Error ...
normalization cellhts2 written 11.9 years ago by Steve Taylor100 • updated 11.9 years ago by ligia@ebi.ac.uk50
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Comment: C: Reading Agilent files using read.maimages
... Hi Misha, > > The files you downloaded from ArrayExpress are in fact in its own > format. For this experiment, in case you might find it useful, we > placed the original Agilent raw data files as given to us by the > submitter at ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/ > ...
written 12.2 years ago by Steve Taylor100
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Comment: C: Reading Agilent files using read.maimages
... Hi, I removed the prefixes from the file headers and they eventually read in. I did get: Read ./E-MEXP-668-raw-data-921408043.txt Read ./E-MEXP-668-raw-data-921408048.txt Read ./E-MEXP-668-raw-data-921408053.txt Read ./E-MEXP-668-raw-data-921408058.txt Error in RG[[a]][, i] <- obj[, columns[[a ...
written 12.2 years ago by Steve Taylor100
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Comment: C: Reading Agilent files using read.maimages
... Hi Sean, >>A typical header for one of these raw files is >> >>CompositeSequence Identifier Database ebi.ac.uk:Database:embl Database ebi.ac.uk:Database:ensembl Database ebi.ac.uk:Database:locus Database ebi.ac.uk:Database:refseq Database >>ebi.ac.uk:Database:ti ...
written 12.2 years ago by Steve Taylor100
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Reading Agilent files using read.maimages
... Hi, I am trying to read a set of Agilent (Human 1A Microarray(V2)[G4110B] (A-AGIL-9)) files from ArrayExpress, accession E-MEXP-668, using read.maimages. I haven't processed Agilent files before (or used read.maimages for that matter!) so sorry if this a basic question but I am wondering if there i ...
survival dyndoc genefilter tkwidgets affy vsn marray convert arrayexpress written 12.2 years ago by Steve Taylor100 • updated 12.2 years ago by Scott Reagan Franklin20
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Comment: C: GSE normalization
... Hi, > I posted a similiar question as you yesterday and my situation is a > little bit different from you: > I have two ideas and one of them is to evaluae the variance across > sites so normalization should not be done for that purpose; but my > second idea needs the normalization, ...
written 12.3 years ago by Steve Taylor100
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GSE normalization
... Hi, I have created 3 separate GSE Objects, read from SOFT format files using GeoQuery. I would like to normalise across experiments using rma. What's the best way to merge the data and then normalise? Ultimately I want to analyse these using limma. Thanks for any help, Steve ...
limma geoquery written 12.3 years ago by Steve Taylor100 • updated 12.3 years ago by Weiwei Shi1.2k
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Technical replicates in limma
... Hi, Apologies if this is a naive limma question but the experimental design in this analysis is quite confusing, which has made me want to confirm the approach with the experts! I have the following set of Affy CEL files that are from 19 treatment samples and 5 control samples. My targets file is ...
probe affy limma written 12.6 years ago by Steve Taylor100
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Research Associate in Applied Statistical Bioinformatics - Oxford University
... Research Associate in Applied Statistical Bioinformatics -------------------------------------------------------- Salary Scale D31 (?20,044- ?30,002) The Computational Biology Research Group (CBRG) is seeking to appoint a three-year Research Associate in Applied Statistical Bioinformatics. The posi ...
written 13.9 years ago by Steve Taylor100 • updated 13.9 years ago by yihong yao40

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Popular Question 11.9 years ago, created a question with more than 1,000 views. For Reading Agilent files using read.maimages

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