User: Guido Hooiveld

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Guido Hooiveld2.2k
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Wageningen University, Wageningen, the Netherlands
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Posts by Guido Hooiveld

<prev • 365 results • page 1 of 37 • next >
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Comment: C: How to process Affymetrix HT HG-U133+ PM Array Plate
... In order to calculate the MAS5-like detection calls (P, A, M), you will need the MM probes. Since you meanwhile know that these are lacking on this PM only array, how could you do this....? Answer: you can't, so what you would like to do makes no sense.... The only alternative I know of that allows ...
written 27 days ago by Guido Hooiveld2.2k
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Comment: C: How to process Affymetrix HT HG-U133+ PM Array Plate
... P-values of what? I assume you would like to compare two or more groups? Use the package limma for this (link), and 'feed' it the normalized data. Please be sure to carefully read the very extensive vignette (manual), since this document contains tons of examples/approaches on how to do this. Also, ...
written 27 days ago by Guido Hooiveld2.2k
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Comment: C: How to make custom CDF file for Clariom D human chip
... What exactly is "RMA-Alt-splicing Normalisation"? Has it to do with the (non-Bioconductor) software 'AltAnalyze'? In any case, I am not familiar with both, but a quick glance at 'AltAnalyze' suggested to me that it makes use of Affymetrix Power Tools (APT), which uses the files than can be downloade ...
written 28 days ago by Guido Hooiveld2.2k
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Answer: A: How to make custom CDF file for Clariom D human chip
... Mmm, did I not basically answer your question in this thread? Here Also, if you did some searching on (for example) this forum you would have learned that for the newest generation of Affymetrix arrays CDF files are not anymore provided (and used). see e.g. here. The packages oligo or xps are the w ...
written 28 days ago by Guido Hooiveld2.2k
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Answer: A: How to process Affymetrix HT HG-U133+ PM Array Plate
... Please familiarize yourselves a little with the design of the Affymetrix arrays. The design of the HG-U133+ PM array differs from the 'original'  HG-U133 Plus 2.0 array at two points, of which this is the relevant one: "Only perfect match (PM) probes from the cartridge design were retained, while mi ...
written 28 days ago by Guido Hooiveld2.2k
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Answer: A: hgu133plus2hsentrezgcdf or hgu133ahsentrezgcdf packages not installing
... Unfortunately biocLite() will not automagically download the custom (remapped) CDF you would like to use from the repository of the MBNI group. You rather have to download them directly by: install.packages("http://mbni.org/customcdf/22.0.0/entrezg.download/hgu133ahsentrezgcdf_22.0.0.tar.gz", type ...
written 29 days ago by Guido Hooiveld2.2k
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Answer: A: how to generate CDF and before normalisation and after normlisation plot for Cla
... No, you should not use / generate a CDF to analyze these arrays. You rather should analyze these type of arrays using the package oligo (link) in combination with the corresponding platform design package (link). In the vignette (PDF) of oligo it is explained how to create the plots you are interes ...
written 4 weeks ago by Guido Hooiveld2.2k
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Comment: C: ReactomePA - Pathway analysis for DE porcine genes
... Likely because Guangchuang did not specify any significance cutoff (he set the cutoffs for both p-value and q-value to 1, i.e. no significance filtering), and you set the p-value cutoff at 0.05 (which is apparently too strict for your experiment). ...
written 5 weeks ago by Guido Hooiveld2.2k
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Comment: C: How to normalize mouse gene 1.0st arry using frma?
... Basically the message tells you what is going on: for the current version of Bioconductor (R-3.4.x) only 3 predefined frozen RMA vectors are available for mouse arrays, i.e. mogene.1.0.st.v1frmavecs, mouse4302frmavecs, and mouse430a2frmavecs. For the arrays you mention these vectors/info isn't avail ...
written 6 weeks ago by Guido Hooiveld2.2k
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Comment: C: How to create a customized OrgDb in order to perform kegga analysis?
... Aha, AFAIK in that case you can use the argument species.KEGG = "ko" when using the function kegga(). Assuming DEGs is a character vector with the differentially expressed KO IDs, something like: k<- kegga(DEGs, species.KEGG = "ko", FDR = 0.05) ...
written 8 weeks ago by Guido Hooiveld2.2k

Latest awards to Guido Hooiveld

Popular Question 10 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Scholar 10 months ago, created an answer that has been accepted. For A: Taking surrogate variable into account before running PCA
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Taking surrogate variable into account before running PCA
Popular Question 10 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: Testing for DE genes
Popular Question 14 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 24 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 24 months ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Supporter 24 months ago, voted at least 25 times.
Centurion 3.9 years ago, created 100 posts.

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