User: Moritz Kebschull

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6 years, 2 months ago
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8 years, 10 months ago
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Posts by Moritz Kebschull

<prev • 10 results • page 1 of 1 • next >
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Gene expression clustering using several dependent samples
... Dear list. I am looking at a dataset comprised of Affy images from disease- affected tissue samples that I am trying to cluster. The problem is that we have 2+ biopsies per study subject, and I am not sure how to best account for their dependency. In contrast to cancer samples, these biopsies diff ...
clustering affy written 6.2 years ago by Moritz Kebschull100
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Design question: How to account for dependent samples?
... Dear list, I am looking at a microarray dataset that consists of 'healthy' and 'diseased' samples from patients with two different diagnoses. We have several 'diseased' samples per patient. For many, but not all patients, a single healthy sample exists (therefore, I cannot do paired analyses withi ...
microarray written 6.6 years ago by Moritz Kebschull100 • updated 6.6 years ago by Gordon Smyth38k
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Answer: A: Problem in SPIA: de must be a vector of log2 fold changes. The names of de shoul
... Dear Adi, dear list, I am trying to run SPIA on some data generated using limma. I am, however, running into an error message I don´t understand - my data (at least to me) look very similar to the "Colorectal" example data set used in the vignette. For the ALL list, I did the following. As ALL_Co ...
written 7.7 years ago by Moritz Kebschull100
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Problem in SPIA: de must be a vector of log2 fold changes. The names of de should be included in the refference array!
... Dear Adi, dear list, I am trying to run SPIA on some data generated using limma. I am, however, running into an error message I don´t understand - my data (at least to me) look very similar to the "Colorectal" example data set used in the vignette. For the ALL list, I did the following. As ALL_Co ...
organism limma spia written 7.7 years ago by Moritz Kebschull100 • updated 7.7 years ago by Tarca, Adi570
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Paired tests using limma and beadarray
... Dear list, I am looking at Illumina beadarrays of 18 patients sampled at baseline ("A") and after intervention ("B"), i.e. a total of 36 arrays. I think in this case, a paired assessment should be done. I am interested in diff. exp. at timepoint B over A. Thus far, I have read the data using the b ...
annotation limma beadarray written 8.4 years ago by Moritz Kebschull100 • updated 8.4 years ago by James W. MacDonald51k
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beadarray: Error when reading control probe profile with readBeadSummaryData
... Dear list, when I try to read the Illumina beadarray control probe profile using readBeadSummaryData library(beadarray) dataFile = "Spag4_data.txt" qcFile = "Spag4_con.txt" BSData = readBeadSummaryData(dataFile = dataFile, dec=",", qcFile = qcFile, skip = 0, qc.skip = 0) I get Error in if (!is.n ...
probe beadarray written 8.7 years ago by Moritz Kebschull100 • updated 8.7 years ago by Mark Dunning1.1k
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Write ExpressionSetIllumina to a file
... Dear list, I am trying to write a normalized ExpressionSetIllumina to a file (for GEO submission). I tried things like write.csv(exprs(BSData.normalised),file="NormalisedData.csv") and got Error in exprs(BSData.normalised) : error in evaluating the argument 'object' in selecting a method for ...
written 8.8 years ago by Moritz Kebschull100 • updated 8.8 years ago by Mike Smith3.9k
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How to extract lfc & p-values for probes identified with a Venn diagram
... Dear list, I am trying to generate a list of probes that are differentially regulated after stimulation in cells with a gene knockdown vs. the wildtype controls. I generated two constrasts and looked at the overlap with a Venn diagram. It looks like this: diff_con(2288(3069)1010)diff_kd I am inte ...
go written 8.8 years ago by Moritz Kebschull100 • updated 8.8 years ago by René Dreos80
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decideTests limitation to certain lfc and p values not working
... Dear list, I am comparing cells with a gene knockdown with wildtype cells to find genes differentially regulated in response to the knockdown using Illumina bead arrays. I plan to compare genes regulated by CPT stimulation in knockdown and wildtype cells. For that, I used a Venn Diagram, and export ...
category beadarray written 8.9 years ago by Moritz Kebschull100 • updated 8.9 years ago by Alex Gutteridge650
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subscript out of bounds error when following new beadarray tutorial
... Dear list, I am trying to follow the new bead-summary tutorial http://www.bioconductor.org/packages/release/bioc/vignettes/beadarray/ inst/doc/beadsummary.pdf However, I end up with a ‘subscript out of bounds’ error. Does anyone happen to know what´s wrong? > library(beadarray) Loading r ...
beadarray written 8.9 years ago by Moritz Kebschull100 • updated 8.9 years ago by Mark Dunning1.1k

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