User: Jarek Bryk

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Jarek Bryk110
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Posts by Jarek Bryk

<prev • 11 results • page 1 of 2 • next >
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Answer: A: Agi4x44Preprocess/Limma and number of significant p-values
... Hi, > This was for one of the datasets, with 2 (four result sets) micorarrays, 1 for each treatment. For another similar dataset, 4 microarrays with 2 samples for each treatment, results are very similar. Could you tell me again how many samples you had per group to compare? And more details ab ...
written 7.1 years ago by Jarek Bryk110
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best annotation package for drosophila (agilent gene expression)?
... Dear group, I am about to analyse Agilent's gene expression data from Drosophila. As far as I checked, there is no *.db annotation file available to be used in conjunction with Agi4x44PreProcess package. I can make one myself (with SQLForge) - I'll probably have to anyway, but I was wondering wheth ...
annotation agi4x44preprocess written 7.2 years ago by Jarek Bryk110
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Comment: C: Agi4x44PreProcess package: Error in build.est
... >> Error in build.eset(tdPROC, targets, makePLOT = FALSE, >> annotation.package = "hgug4112a.db") : >> rownames in pData(targets) different from colnames RGlist$G >The error message indicates that you don't have the same number of samples data (tdPROC: colnames RGlist$G) as yo ...
written 7.2 years ago by Jarek Bryk110
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Comment: C: GO enrichement and Ensembl ID
... On 12/05/2011 19:38, mjonczyk at biol.uw.edu.pl wrote: > you can use ontologizer (java application, not in bioconductor). > http://compbio.charite.de/index.php/cmdlineOntologizer.html Or you can use web-based GeneTrail http://genetrail.bioinf.uni-sb.de/ (no need to prepare an association file ...
written 7.6 years ago by Jarek Bryk110
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Comment: C: retrieve genes names after KEGG hypergeometric test
... Hello, the problem is as in the subject, and here are the details: > class(RG) [1] "RGList" attr(,"package") [1] "limma" > library(arrayQualityMetrics) > library(convert) > x=as(RG,"NChannelSet") > class(x) [1] "NChannelSet" attr(,"package") [1] "Biobase" > arrayQualityMetrics(x, ...
written 8.1 years ago by Jarek Bryk110
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how to import Agilent CGH custom design xml file into limma
... Hello, I am trying to analyse my two-color mouse aCGH data on Agilent platform. I have custom-designed 1M probe CGH arrays for which I have a xml file that defines the arrays' design (layout etc.). My goal (for now) is to identify CNVs in the samples. I am trying to use snapCGH to analyse the sampl ...
acgh cgh probe snapcgh written 8.2 years ago by Jarek Bryk110 • updated 8.2 years ago by Sean Davis21k
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plotting multiple genes on a genome
... Hello, I would like to plot a list of interesting genes (located on different chromosomes) on a genome. I extracted their genomic coordinates with biomaRt (see table below) and now I am looking for a way to send them all to some plotting function. So I have a matrix like this: c ...
written 9.2 years ago by Jarek Bryk110 • updated 9.2 years ago by Oosting, J. PATH550
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only 9-digit refseq IDs when using custom CDF for mouse4302 array
... Hello, I am not sure if this is a problem, but here we go. When I analyse my Affy mouse4302 data using custom CDF file from the Dai lab that collapses probe/sets onto RefSeq IDs: > affy.batch.object at cdfName<-"Mouse4302_Mm_REFSEQ" I only get 9-digit RefSeq IDs, and none of the more commo ...
go mouse4302 cdf affy written 9.2 years ago by Jarek Bryk110
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Answer: A: courses
... Jonathan Sive wrote: > Does anyone know of any introductory courses in R and Bioconductor > packages coming up soon in the UK? MBO Practical Course on Analysis and Informatics of Microarray Data 12-17, October 2009 EBI-EMBL, Hinxton, Cambridge, UK http://www.ebi.ac.uk/microarray/General/Ev ...
written 9.3 years ago by Jarek Bryk110
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comparing affymetrix and agilent microarray data
... Hello again, I have two datasets acquired by running the same samples from two populations on both affymetrix and agilent (single-color) microarrays. I want to find genes that are consistently differentially expressed between the two populations in both platforms. For analysis of the affymetrix da ...
cdf probe affy written 9.6 years ago by Jarek Bryk110

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