User: BioMed

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BioMed40
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Posts by BioMed

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Comment: C: Abnormal outcome when re-analyzing GEO microarray data?
... Yes, I agree with your opinion. When searching around, we can also see similar cases, GSE26511, for example. ...
written 3 months ago by BioMed40
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Comment: C: Abnormal outcome when re-analyzing GEO microarray data?
... Thank you for your nice feed back. It is quite strange that we can't get any DEGs when using adjusted P-value, right? When searching for similar cases (early vs late, progressive vs non-progressive, etc.), I also faced the same situation. I wonder is it a biological or a statistical problem? ...
written 3 months ago by BioMed40
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Comment: C: Abnormal outcome when re-analyzing GEO microarray data?
... My protocol is quite similar to the authors. However, they stated that they used P-value < 0.01 as the significant level, not adjusted P-value. ...
written 3 months ago by BioMed40
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Comment: C: Abnormal outcome when re-analyzing GEO microarray data?
... Thanks, I improved it. ...
written 3 months ago by BioMed40
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Abnormal outcome when re-analyzing GEO microarray data?
... Dear all, When I re-analyzed several data sets, I got 0 significant genes regarding the adjusted p-value (Benjamini-Hochberg correction). The adjusted p-values of these data sets are close to 1, but the original papers stated they found significant results. There are more than one cases but I here ...
gene R microarray written 3 months ago by BioMed40
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Comment: C: The same Illumina expression data gathered by GEOquery and direct download shows
... Thank you very much for pointing it out. We should be careful when using getGEO when gathering Illumina arrays then. ...
written 3 months ago by BioMed40
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The same Illumina expression data gathered by GEOquery and direct download shows different value after normalization?
... Dear all, I have one question that needs your help. Suppose that I need to process GSE39340 data set. M1. I used GEOquery to get the data and normalized it by the below commands: library(GEOquery) library(lumi) eset <- getGEO("GSE39340") lumi.N.Q <- lumiExpr ...
preprosessing illumina normalization written 3 months ago by BioMed40 • updated 3 months ago by andrew.j.skelton733.9k
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Comment: C: Need help in preprocessing Illumina HumanHT-12 V4.0 expression beadchip
... Thank you very much. I will try to use lumi. ...
written 4 months ago by BioMed40
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Need help in preprocessing Illumina HumanHT-12 V4.0 expression beadchip
... Dear all, So far, I've been working with Affymetrix-based microarray. Nevertheless, my new project requires processing the data generated from Illumina HumanHT-12 V4.0 expression beadchip. Please let me know or give me some tips about what should I do to get a ready-to-use spreadsheet file from the ...
gene expression microarray written 4 months ago by BioMed40 • updated 4 months ago by Agaz Hussain Wani40
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Comment: C: A question on microarray-based validation study
... Thank you for your advice. I will start to learn limma and kernlab. ...
written 8 months ago by BioMed40

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