User: Mike Walter

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Mike Walter230
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Posts by Mike Walter

<prev • 23 results • page 1 of 3 • next >
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Comment: C: eset -Affy Mouse Gene 1.0 ST. Array-
... Hi Benilton, Thank you very much. I'll go and update my R Version. Kind regards, Michael -- Dr. Michael Walter MFT Services University of T?bingen Calwerstr. 7 72076 T?bingen Tel.: +49 7071 29 83210 Fax. + 49 7071 29 5228 web: www.mft-services.de Confidential ...
written 7.2 years ago by Mike Walter230
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Comment: C: eset -Affy Mouse Gene 1.0 ST. Array-
... Dear List, I have a set of the new AraGene 1.1-st arrays and thus like to build a corresponding pdInfo package. Anyway, I get an error while creating the package. Please see code and error mesasge below. Obviously, the mps file for the array can't be found, and I was unable to figure ...
written 7.2 years ago by Mike Walter230
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Comment: C: Overlapping boxplots with transparency
... Dear List, I'd like to use maanova to analyze a set of 64 affy arrays (U219). The samples are from 8 donors (4x male and female each), which where taken in a short timecourse (T0-T3) both treated and untreated. I'm interested transcripts that are affected by the treatment and especially in those t ...
written 8.3 years ago by Mike Walter230
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Answer: A: Paired Data in maSigPro
... Dear Maria, Thanks for your answer. I allready thought that this might be your answer. In the meantime I run maSigPro with the design posted in the previous mail and the results look quite promising. However, yesterday I had the idea to simply subtract the t0 signal from the other time points for e ...
written 8.6 years ago by Mike Walter230
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Paired Data in maSigPro
... Dear List, I have a tiem series experiment, I want to analyse with maSigPro. The data are from blood samples from 8 donors taken at 4 different timepoints under 2 treatments. My design matrix would look like this: > dm Time Replicate Control LPS I10R029a01.CEL 0 1 1 0 I10R02 ...
masigpro written 8.6 years ago by Mike Walter230
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retrieve genes names after KEGG hypergeometric test
... Hi Cl?mentine, The "db" just adds a ".db" suffix to load the library. Just try paste(yourDb, "db", sep="."). This will give "yourDb.db". Maybe a short example will help. There is a list of 8 probesets from tha affy rat 230 2.0 array. I'm looking which of these transcripts are involved in the KEGG p ...
annotation pathways go rat2302 probe affy category written 8.7 years ago by Mike Walter230 • updated 8.7 years ago by Iain Gallagher930
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Comment: C: Getting annotation into eset
... Hi Cl?mentine, I don't know, if such a function exists. I use two little helper functions to retrieve probe IDs or gene symbols of genes in a genelist, that are associated with a KEGG ID: KEGG2genes = function(KEGGID, genelist, db){ require(paste(db, "db", sep="."), character.only = TRUE) l = ve ...
written 8.7 years ago by Mike Walter230
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Comment: C: remove microarray batch effects using Limma
... Hi Moshe, Hi Zhi, I had some data with strong batch effects a while ago. I used several methods (e.g. adding the batch as factor in the modeling or Combat). In the end I decided to use Combat, which works quite nice. However, I wasn't aware of the removeBatchEffect() function so I just got curious. ...
written 8.7 years ago by Mike Walter230 • updated 22 months ago by Gordon Smyth37k
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Answer: A: arrayQualityMetrics 3.2.0 in Bioc release 2.7 is broken
... Dear List, I have a series of golden gate cancer panel SNP data and wanted to use the beadarraySNP package to analyse the data. Unfortunately, I only have the idat files and not the csv files. Thus I tried 'crlmm' package to parse the idats for the red and green channel to create the csv tables. I ...
written 8.7 years ago by Mike Walter230
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Comment: C: AgiMicroRna problems
... Hi Jim, Thanks for your answers. This makes everything clear now. And best of all, my GO enrichment is not wrong, which was my first fear. Kind regards, Mike -----Urspr?ngliche Nachricht----- Von: "James W. MacDonald" Gesendet: 01.10.2010 15:43:14 An: "Mike Walter" Betreff: Re: [BioC] GOStats: ...
written 8.8 years ago by Mike Walter230

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