User: Guido Hooiveld

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Guido Hooiveld2.4k
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Wageningen University, Wageningen, the Netherlands
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Posts by Guido Hooiveld

<prev • 398 results • page 1 of 40 • next >
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Answer: A: error after normalizing data
... Hi, Since you didn't post any code, we have to guess what you did, and what you would like to achieve.... However, based on the very brief error message I assume you are analyzing an HTA array data set. I would suggest to have a look at this thread, in which some code is given that can get you start ...
written 1 day ago by Guido Hooiveld2.4k
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Comment: C: project miran packages
... The error you got: All the CEL files must be of the same type. is rather self-explanatory. It means that either a) you have an experiment consisting of some CEL files that you **think** are mirna 3.0 arrays, but rather are (all) of a different type; or b) that your CEL files are of 'mixed or ...
written 7 days ago by Guido Hooiveld2.4k
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Answer: A: project miran packages
... Affymetrix (and hence Bioconductor) doesn't provide a chip definition file (CDF) for this type of array. To process your CEL files you will need the `oligo` package ([here][1]) and corresponding platform design package ([here][2]). You may want to check e.g. this post of James McDonald ([here][3]) f ...
written 8 days ago by Guido Hooiveld2.4k
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Answer: A: run affy package encounts clariomdhumancdf error
... As said in the related thread started by you, and that now is deleted (also by you?!), these are 3rd generation Affymetrix arrays for which NO Chip Definition File (CDF) is available. As a result, these arrays can NOT be analyzed using the library `affy`, but rather should be analyzed using `oligo` ...
written 16 days ago by Guido Hooiveld2.4k
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Answer: A: run LIMMA package encounts clariomdhumancdf error
... There are several issues regarding your question: - you didn't post the full code you used to obtain object `data.raw`. - `limma` as such doesn't have functionality to preprocess (normalize) Affymetrix arrays (CEL files); you will have to do this separately using functionality available in the libr ...
written 19 days ago by Guido Hooiveld2.4k
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Comment: C: justRMA and wrong customCDFs causing segfault
... Well, in my case it works fine using the R-3.5.1 and BioC3.8... Using some (9) mouse mogene1.1 arrays in combination with a custom CDF: > install.packages("http://mbni.org/customcdf/23.0.0/entrezg.download/mogene11stmmentrezgcdf_23.0.0.zip", repos=NULL) trying URL 'http://mbni.org/cust ...
written 7 weeks ago by Guido Hooiveld2.4k
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Is GCRMA normalization possible with oligo?
... I am updating my analysis pipeline for Affymetrix arrays, and would like to use the library `oligo` for the analysis of all types/generations of arrays. Until now I used the functionality of the library `affy` to normalize the 1st generation of arrays (those arrays including MM probes), and usually ...
normalization gcrma oligo affymetrix pd.moe430a written 9 weeks ago by Guido Hooiveld2.4k • updated 9 weeks ago by James W. MacDonald49k
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Comment: C: Ensembl plants at annotationHub?
... Thanks! Meanwhile downloaded the file and everything is working fine.   ...
written 3 months ago by Guido Hooiveld2.4k
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Comment: C: Ensembl plants at annotationHub?
... Hi Johannes, Thanks for your offer! As far as I am concerned only an EnsDb for the latest genome info for Arabidopsis would do for now. (EnsemblPlants, release 41, Sept 2018, here). Thanks a lot for your help! Guido ...
written 3 months ago by Guido Hooiveld2.4k
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Ensembl plants at annotationHub?
... Hi, I am regularly using the annotationHub to retrieve/query the Ensembl-based gene annotations (ensembldb). This works fine for e.g human and mouse, but I now would like to obtain info made available through the Ensembl Plant database; specifically for Arabidopsis ( http://plants.ensembl.org/Arabi ...
arabidopsis thaliana annotationhub ensembl ensembldb plant written 3 months ago by Guido Hooiveld2.4k • updated 3 months ago by Johannes Rainer1.4k

Latest awards to Guido Hooiveld

Scholar 3 months ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
Scholar 4 months ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
Popular Question 6 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 8 months ago, created a question with more than 1,000 views. For Design and contrast question limma (additive or nested or duplicateCorrelation())??
Popular Question 9 months ago, created a question with more than 1,000 views. For How to retrieve 'conservation score' sequence?
Popular Question 21 months ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Scholar 21 months ago, created an answer that has been accepted. For A: Queries around makeOrgPackageFromNCBI
Scholar 21 months ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
Popular Question 21 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 21 months ago, created a question with more than 1,000 views. For problem generating Chinese hamster txdb from GFF file
Popular Question 21 months ago, created a question with more than 1,000 views. For minfi, bumphunter + complex experimental design, and 3 other 450K queries
Popular Question 21 months ago, created a question with more than 1,000 views. For package/function for median center & unit variance
Popular Question 21 months ago, created a question with more than 1,000 views. For limma: one sample t-test + covariate
Popular Question 21 months ago, created a question with more than 1,000 views. For Design and contrast question limma (additive or nested or duplicateCorrelation())??
Popular Question 21 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Taking surrogate variable into account before running PCA
Scholar 21 months ago, created an answer that has been accepted. For A: Taking surrogate variable into account before running PCA
Popular Question 21 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: Testing for DE genes
Popular Question 2.1 years ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 2.9 years ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 2.9 years ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Supporter 2.9 years ago, voted at least 25 times.
Centurion 4.8 years ago, created 100 posts.

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