User: theobroma22

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theobroma22390
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Posts by theobroma22

<prev • 75 results • page 1 of 8 • next >
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Comment: C: Figure out outliers in microarray dataset with z-scores
... Ok, please give me some time to provide this to you. In the meantime I found this slide deck that also has R code in it. http://compdiag.molgen.mpg.de/ngfn/docs/2005/sep/beissbarth_cDNA_QCPP.pdf A QQ plot is also show. I'll send you a sample R code to do the qqplot soon. Thanks. ...
written 17 hours ago by theobroma22390
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Comment: C: Figure out outliers in microarray dataset with z-scores
... The QQ technique used is the typical QQ technique. You qqplot the residuals or the p-values of the linear model of the microarray analysis, like control v. Tmt or timecourse analysis. Then, those that off the line at either end are your outliers. Or do you mean R code? ...
written 1 day ago by theobroma22390
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Comment: C: GC percent detection for several number of genes
... If you have any nucleotide sequence, one could just use geneboy, and not worry about if it's exonic, UTR, promoter or other. https://www.dnalc.org/resources/geneboy.html ...
written 2 days ago by theobroma22390
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Comment: C: GC percent detection for several number of genes
... OP said he has 400 "genes" and needs to calculate gc content, so yes the oligo package can be employed. OP didn't say he needed the sequences. My bad! ...
written 2 days ago by theobroma22390
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Comment: C: Figure out outliers in microarray dataset with z-scores
... You can use PCA but it's generally not used to find outliers. And yes, I've used QQ for microarray analysis. ...
written 2 days ago by theobroma22390
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Answer: A: GC percent detection for several number of genes
... Can you use R? The oligo package can do this for you, among many other ways. Also, in Excel. ...
written 2 days ago by theobroma22390
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Answer: A: Figure out outliers in microarray dataset with z-scores
... If it's in a book I would think it's acceptable to use resistant z-score. Another way to view outliers is the Q-Q plot. ...
written 2 days ago by theobroma22390
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Comment: C: converting mutual information matrix to gene regulatory network
... Ok. Scroll down to the bottom of grn and send me a screenshot. And scroll all the way to the right and send me a screenshot. According to you all 192 observations in grn are miRNAs? ...
written 2 days ago by theobroma22390
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Comment: A: converting mutual information matrix to gene regulatory network
... I looked at your screenshots. If your miRNAs have "disappeared" how is it that both MI and grn are the same size? I expected grn to be "smaller" than MI. ...
written 2 days ago by theobroma22390
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Comment: C: converting mutual information matrix to gene regulatory network
... First you need to download the file to the local folder, then in R use the above command. ...
written 2 days ago by theobroma22390

Latest awards to theobroma22

Rising Star 4 days ago, created 50 posts within first three months of joining.
Scholar 7 days ago, created an answer that has been accepted. For A: Creating a targets matrix
Scholar 14 days ago, created an answer that has been accepted. For A: Creating a targets matrix
Scholar 6 weeks ago, created an answer that has been accepted. For A: Creating a targets matrix
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Creating a targets matrix

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