User: Guido Hooiveld
Guido Hooiveld • 2.3k
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- 11 years, 7 months ago
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Posts by Guido Hooiveld
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... FYI: Johannes' solution is automagically performed within the tximport function when specifying the argument ignoreTxVersion = TRUE (default = FALSE).
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written 1 day ago by
Guido Hooiveld • 2.3k
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... at the help page of ReadAffy (found by ?ReadAffy) find the option 'compress':
compress: are the CEL files compressed?
Thus (assuming the last file in your list (GSM1293830_19_10_Control_108h.CE) has a wrong extension because of an incomplete copy/paste error):
AffyData <- ReadAffy(filenam ...
written 13 days ago by
Guido Hooiveld • 2.3k
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... Your code is working for me. I used as input the 12 UMA IDs above.
Although not directly related to the problem your reported, please note that the function enrichKEGG() is used to check which KEGG pathways are over-represented in a list of selected genes, e.g. identified by an differential gene ex ...
written 19 days ago by
Guido Hooiveld • 2.3k
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... Mmm, looks like you have a mix of release and development packages.... For R-3.5.x / Bioc-3.7 you should use clusterProfiler version 3.8.1 (here) (2nd number = an even number) , you have version 3.9.1 (2nd number = an odd number, thus the 'development' version). Maybe this explains your error; again ...
written 8 weeks ago by
Guido Hooiveld • 2.3k
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Comment:
C: Guidance to handle .CEL file in R
... To add to Bioconductor workflows linked to by Lori: the Affymetrix workflow at the F1000 here is also a good starter; for online QC analysis ArrayAnalysis.org might be handy.
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written 8 weeks ago by
Guido Hooiveld • 2.3k
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... You did not define the object de, which you used as input. Also, the last line of your code is weird; why do you include head(summary(xx))?
Example from vignette is running fine for me (please note my comments):
> library(clusterProfiler)
> data(geneList, package='DOSE')
> de <- na ...
written 8 weeks ago by
Guido Hooiveld • 2.3k
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... Did you prepare the input files yourselves? I.e. fSym, fChr, and fGO? Could you show the content of these files using head()?
How did you conclude that it didn't work? Could you show some code and sessionInfo()?
As a side note: please be informed that through the AnnotationHub a pre-made OrgDb ...
written 8 weeks ago by
Guido Hooiveld • 2.3k
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... I just noticed that in Salmon version 0.11.0 a fix has been applied to correct a bug that for multi-isoform genes resulted in the wrong calculation of lengths and effective lengths of genes. Although this was, according to the release notes, (apparently) *only* an issue when these numbers were calcu ...
written 9 weeks ago by
Guido Hooiveld • 2.3k
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Comment:
C: Pathview results interpretation
... It would have been helpful if you also posted your code and/or graph, because now we have to *assume* the things you did... Anyway, if I plot/overlay my gene expression data using pathview, rectangles correspond indeed to genes/enzymes. If you plot fold changes, red is 'increased', and green is 'dec ...
written 3 months ago by
Guido Hooiveld • 2.3k
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Comment:
C: Affe package mas5 error
... It's working fine for me using some similar old (1st generation) mouse arrays that I had at hand.
However, I noticed that you are using version 18 of the custom CDF, which was released more than 4 years ago.... Maybe these old CDFs are not compatible anymore with the current version of R/BioC? The ...
written 3 months ago by
Guido Hooiveld • 2.3k
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