User: giroudpaul

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giroudpaul30
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New User
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France
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1 week, 3 days ago
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1 year, 8 months ago
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Posts by giroudpaul

<prev • 38 results • page 1 of 4 • next >
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Comment: C: pd.hta.2.0 not installed with Bioconductor 3.5 BiocInstaller 1.26.0 R 3.4.1
... Your answer seems to be here : Error: package or namespace load failed for 'oligoClasses' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called 'iterators' Error : package 'oligoClasses' could not be loaded ERROR: lazy loading failed for package 'pd.hta. ...
written 3 months ago by giroudpaul30
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Comment: C: HTA 2.0 and Transcript level analysis
... "The ChipDb package only has one real table, which maps the probeset ID to the Entrez Gene ID, and any other lookups will be farmed out to the org.Hs.eg.db package." This is what I refered to when saying this. As you said, Affymetrix is not providing Transcript detailed information for the ChipDB p ...
written 3 months ago by giroudpaul30
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Comment: C: HTA 2.0 and Transcript level analysis
... Thank you very much for these explanations. As I suspected, it had something to do with how the ChipDB package is built. Thank you for your time, Paul ...
written 3 months ago by giroudpaul30
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Comment: C: HTA 2.0 and Transcript level analysis
... Hi again, So I annotated my dataset just to have a look, and it seems that the hta20probeset.db does not really differentiate between transcripts as it maps all refseq transcripts for one gene to each probes corresponding to this gene. For example: hta.dat = rma(hta.dat, target="probeset") Probes ...
written 3 months ago by giroudpaul30
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HTA 2.0 and Transcript level analysis
... Dear Bioconductor members I am asked to analyze my lab's HTA2.0 data once again, but this time to find information on specific transcript variants. Do you know if it is possible to annotate an Eset obtained via : data.rma = oligo::rma(data, target="probeset")? For what I understand, this apply RMA ...
transcripts hta2.0 written 3 months ago by giroudpaul30
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Comment: C: Meta-analysis of microarrays (and RNA-seq) data
... Hello Alex, So I had some time to look up crossmeta and I ran into some troubles trying to follow the vignette. I also have some additional questions about the package and what it can do, so would it be possible to contact you in private ? ...
written 6 months ago by giroudpaul30
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Comment: C: Meta-analysis of microarrays (and RNA-seq) data
... Well thank you for your answer, sorry for replaying this late. I didn't had time to go further on my investigations in the different packages I cited, as I am in sick leave at the moment, but I planned on understanding which package was the more suitable. Thank you for your explanation, it give me ...
written 7 months ago by giroudpaul30
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Meta-analysis of microarrays (and RNA-seq) data
... Dear Bioconductor Scientists, I am rather new to NGS data analysis, I learned what I know all by myself as there is no bioinformaticians where I work. Nevertheless, I already analyzed my own affymetrix HTA 2.0 data, as well as a couple public data on affymetrix HGU133 and Illumina HumanHT12 V3/4 m ...
meta-analysis written 8 months ago by giroudpaul30 • updated 7 months ago by alexvpickering80
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Comment: C: Error with boxplot command from oligo package with raw Affy data
... Well, I also learned something then, it's much easier this way ...
written 8 months ago by giroudpaul30
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Comment: C: Error with boxplot command from oligo package with raw Affy data
... I don't want to say something wrong as I am myself also a beginner, but I think the problem lies that to use the boxplot fonction of oligo, you need to use data coming from the oligo::rma (even if not normalized yet), because you need to select the "Level of summarization (only for Exon/Gene arrays) ...
written 8 months ago by giroudpaul30

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