User: Guido Hooiveld

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Guido Hooiveld2.0k
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Wageningen University, Wageningen, the Netherlands
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Posts by Guido Hooiveld

<prev • 301 results • page 1 of 31 • next >
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bug limma / illuminaio? Otherwise small feature request...
... It seems I found a small bug in limma or illuminaio. If not, when the behavior below is as intended, please allow me to put forward a (small) feature request: the possibility to also read compressed IDAT files (just like it is possible for compressed BGX files).   -> at the Gene Expression Omn ...
limma illuminaio idat gzip written 5 days ago by Guido Hooiveld2.0k • updated 5 days ago by Matthew Ritchie630
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Comment: C: Probeset ID's to entrez for Clariom D Human Affy Array
... Did you read the this full thread? Also the comments of James below? "The easiest thing to do is to use annotateEset in my affycoretools package". Some relevant points: - you can summarize the probes on the levels of known transcripts (= core; default), or on the level of probe set regions, that ...
written 9 days ago by Guido Hooiveld2.0k
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Comment: C: Testing for DE genes
... Had few spare minutes left.... so I quickly analyzed this data set. Regarding Aaron's final conclusion: if you create an MDS plot using limma's plotMDS function, you indeed see the treatment groups don't nicely separate. Hence, not surprising that only few probe sets are differentially expressed.... ...
written 9 days ago by Guido Hooiveld2.0k
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Answer: A: Illumina methylationEPIC demo data in IDAT format?
... Why not check GEO whether such data set exist? All samples submitted that were analyzed on this array: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21145 One of the experiments that has the idat files: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92579   ...
written 12 days ago by Guido Hooiveld2.0k
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Answer: A: simple affy: covdesc file in directory, but cant get raw.data <- read.affy () co
... Please have a close look at the error that is returned: cannot open file './covdesc': No such file or directory. Combine this with the info on the help page (?read.affy): Usage: read.affy(covdesc = "covdesc",path=".", ...)   In your case you are using a covariate description file that has the e ...
written 21 days ago by Guido Hooiveld2.0k
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Answer: A: annotation in microarray analysis
... First a general comment: please note that the workflow you used is rather old (June 2011), and it is likely that the functionality of Bioconductor packages has been changed over the years. In that respect maybe also helpful to check out this more current workflow at the F1000 Bioconductor channel he ...
written 23 days ago by Guido Hooiveld2.0k
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Comment: C: RNA degradation plot for GeneChip Mouse Gene 2.0 ST Array
... To analyze your data set you likely copied all of James's code above "as is". Then you also copied this line: whatevs2 <- sapply(1:36, function(x) rowMeans(do.call(cbind, lapply(whatevs, function(y) log2(vals[y,x]))))) The problem is the number 36; as James indicated this line of code iterates ...
written 7 weeks ago by Guido Hooiveld2.0k
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Answer: A: error in getsymbol function
... Without providing more code it is rather difficult to help, but: - the error message indicates that the object probeset.list$ID is empty. - you are using an outdated interface to query annotation databases; you'd better either use select() or mapIds(). See ?select or ?mapIds after loading the libr ...
written 7 weeks ago by Guido Hooiveld2.0k
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Answer: A: Python Module from Kim and Volsky (2005) PAGE: Parametric Analysis of Gene Set E
... FYI, since you ask at the Bioconductor forum: I know that the PAGE algorithm has been implemented in the package PGSEA. ...
written 8 weeks ago by Guido Hooiveld2.0k
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Comment: C: How does the org.Dm.eg.db package deal with NOT annotation qualifiers when anno
... For human few proteins the NOT qualifier is also used, but this is only for a small percentage (1281 out of 409697 entries). Whether this is taken into account in the annotation packages (org.Xx.eg.db or GO.db), and if so how, is a good question! I don't know....   > GAF <- read.delim(gzfil ...
written 9 weeks ago by Guido Hooiveld2.0k

Latest awards to Guido Hooiveld

Commentator 9 days ago, created a comment with at least 3 up-votes. For C: Testing for DE genes
Popular Question 3 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Supporter 13 months ago, voted at least 25 times.
Popular Question 13 months ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Popular Question 13 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Centurion 3.0 years ago, created 100 posts.

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