User: Guido Hooiveld
Guido Hooiveld • 2.0k
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- Wageningen University, Wageningen, the Netherlands
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- 2 days, 14 hours ago
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- 10 years, 3 months ago
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Posts by Guido Hooiveld
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... 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 ...
written 5 days ago by
Guido Hooiveld • 2.0k
• updated 5 days ago by
Matthew Ritchie • 630
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... 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 Hooiveld • 2.0k
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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 Hooiveld • 2.0k
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... 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 Hooiveld • 2.0k
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... 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 Hooiveld • 2.0k
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... 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 Hooiveld • 2.0k
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... 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 Hooiveld • 2.0k
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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 Hooiveld • 2.0k
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116
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... 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 Hooiveld • 2.0k
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... 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 Hooiveld • 2.0k
Latest awards to Guido Hooiveld
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Popular Question
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For LIMMA: warning coercing argument of type 'double' to logical
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13 months ago,
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For import DOT (GraphViz) into Cytoscape
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