User: giroudpaul

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giroudpaul30
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New User
Location:
France
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1 day, 9 hours ago
Joined:
1 year, 2 months ago
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Posts by giroudpaul

<prev • 33 results • page 1 of 4 • next >
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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 13 days 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 6 weeks 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 11 weeks ago by giroudpaul30 • updated 8 weeks 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 11 weeks 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 11 weeks ago by giroudpaul30
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Comment: C: Trouble annotating HTA microarray
... Thanks, that's nice to see such rapid support and fix ! I will look it up. ...
written 11 months ago by giroudpaul30
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Trouble annotating HTA microarray
... Dear bioconductor members, I finally got my hands on results of HTA 2.0 microarray experiments, and I started processing them using the standard methods. Reading CEL files, and performing RMA doesn't pose problems, for RMA I used oligo this way : > data.rma = oligo::rma(data, background=TRUE, ...
hta pd.hta.2.0 hta20sttranscriptcluster.db written 11 months ago by giroudpaul30 • updated 11 months ago by James W. MacDonald43k
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Comment: C: Annotating the Human Gene 2.0 ST Array annotate with hugene20sttranscriptcluster
... you may try the pd.hugene.2.0.st which provide all the annotations for the platform, I found it easier as a non expert. But for the explication, I will suggest you look at the reference manual of each of theses package, it tell exactly what they do. ...
written 11 months ago by giroudpaul30
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Comment: C: converting amino-acid one letter code into cDNA sequene
... Well it's easier to convert a DNA sequence into protein sequence. Here you will face a problem, caused by the Genetic Code redundancy (see https://en.wikipedia.org/wiki/Genetic_code#RNA_codon_table) In other words, one amino acide can be coded by different DNA codons. Thus, if you want to create ...
written 12 months ago by giroudpaul30
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Comment: C: TopTable Problem : Unique Adj.P.Val which is near 1
... Well I checked the PCA plot yesterday after our talk, and this confirmed tour statements that the dataset was rubbish. I didn't understood that they were using unadjusted P in the paper (though they just simplified the term, but meant the adjusted p.val). Thanks for the salvation code, sadly, the 6 ...
written 12 months ago by giroudpaul30

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