User: Guido Hooiveld

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Guido Hooiveld2.5k
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Wageningen University, Wageningen, the Netherlands
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Posts by Guido Hooiveld

<prev • 409 results • page 1 of 41 • next >
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Answer: A: Microarray Data Analysis CDF Problem
... Hi, First some remarks: Use indeed only the package `oligo` to read and process these files, and not `affy`. There is indeed no CDF available for the HuGene ST 1.1 arrays! That's why you need the `oligo`-based framework with the corresponding PlatformDesign `(PdInfo`) info package! gcRMA normalizat ...
written 1 day ago by Guido Hooiveld2.5k
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Comment: C: Inconsistent results when normalizing HTA2.0 arrays at "level=core"
... Thanks James, got it! Regarding putting it on a TODO list: on one hand, for the reasons you explained above, I agree it may feel it hasn't high priority. On the other hand, because these arrays can only be processed through the `oligo` framework, and within `oligo` only the function `fitProbeLevelMo ...
written 12 days ago by Guido Hooiveld2.5k
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Inconsistent results when normalizing HTA2.0 arrays at "level=core"
... I noticed an intriguing discrepancy when I normalized a set of HTA2.0 arrays (GSE111156, [here][1]). Specifically, a different number of probesets is returned when using the `rma` or `fitProbeLevelModel` function in `oligo`, even if in both cases the argument `target=core` is used. I initially notic ...
affycoretools oligo rma hta2.0 fitprobelevelmodel written 13 days ago by Guido Hooiveld2.5k • updated 13 days ago by James W. MacDonald50k
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Comment: C: u133aaofav2 platform gcrma Normalization
... This has been asked here before. As far as I know Affymetrix has never released the probe information file for this array, and therefore it could not made available at Bioconductor. gcRMA normalization is thus not possible (in principle). See e.g. here: [link][1]. However, it has been suggested by ...
written 20 days ago by Guido Hooiveld2.5k
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Comment: C: rma summarization error when normalizing using oligo and brainarray cdf
... Yes, you are correct! `raw_data`: The assayData of this object reflect the number of probes (not probesets) present on the array. This number is independent of the 'chip definition file' (i.e. probe-to-probeset mapping) that is used. Hence these are the same for `raw_data` and `raw_data2`. In the ...
written 22 days ago by Guido Hooiveld2.5k
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Comment: C: How to find out the genes that changes in expression by using gene level express
... Next to the very useful case studies in the `limma` user guide, a good read to get started is also this workflow at the F1000: https://f1000research.com/articles/5-1384 Be sure to first study the case studies, though! ...
written 29 days ago by Guido Hooiveld2.5k
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Answer: A: Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
... You didn't post your complete code, but have you assigned some IDs (probeset IDs resp. EntrezGene IDs) to the (your) 'variables' PROBEID resp. ENTREZID? I am asking because you code as such should work....(see below). Two remarks: I wouldn't recommend naming your variable that contains the probe/ent ...
written 10 weeks ago by Guido Hooiveld2.5k
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Comment: C: Annotation of Rice Affymatrix Data
... Please be more specific. Which rice array? There are 3 types sold by Affymetrix... How did you normalize the data? Please provide your code. BTW: I noticed that you tagged your post as a job advertisement, which is obviously not the case... Please remove that tag. ...
written 11 weeks ago by Guido Hooiveld2.5k
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Comment: C: GSEABase: how to extract shortDescription from GeneSetCollection object
... Thanks Martin for your hints. Using the function `description` indeed does the trick! > description(GeneSets[[2]]) [1] "KEGG: MAPK signaling pathway" > ...
written 11 weeks ago by Guido Hooiveld2.5k
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GSEABase: how to extract shortDescription from GeneSetCollection object
... Hi, I am using the package `GSEAbase` to import a GMT file (file with gene sets). This is working fine, but I don't understand how I can extract the 'shortDescription' of the gene sets from the `GeneSetCollection`-object. I assumed this could be done using the function `shortDescription`, but appare ...
gseabase written 11 weeks ago by Guido Hooiveld2.5k • updated 11 weeks ago by Martin Morgan ♦♦ 23k

Latest awards to Guido Hooiveld

Popular Question 6 months ago, created a question with more than 1,000 views. For Design and contrast question limma (additive or nested or duplicateCorrelation())??
Scholar 6 months ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: run affy package encounts clariomdhumancdf error
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: run LIMMA package encounts clariomdhumancdf error
Popular Question 6 months ago, created a question with more than 1,000 views. For limma - technical replicates: duplicateCorrelation() or avereps()?
Popular Question 6 months ago, created a question with more than 1,000 views. For Illumina 450K + CHARM/dmrFinder
Popular Question 6 months ago, created a question with more than 1,000 views. For package/function for median center & unit variance
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Popular Question 6 months ago, created a question with more than 1,000 views. For biomaRt: how to retrieve the MOUSE gene symbol?
Popular Question 6 months ago, created a question with more than 1,000 views. For KEGG REST: retrieving genes
Scholar 6 months ago, created an answer that has been accepted. For A: run affy package encounts clariomdhumancdf error
Scholar 7 months ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
Scholar 8 months ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
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Scholar 2.0 years ago, created an answer that has been accepted. For A: Queries around makeOrgPackageFromNCBI
Scholar 2.0 years ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
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