## User: apfelbapfel

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Last seen:
4 months ago
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1 year, 2 months ago
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a**********@gmx.de

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#### Posts by apfelbapfel

<prev • 11 results • page 1 of 2 • next >
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... My apologies for unclear terminology. You are absolutely correct, the number of genes goes down from around 46000 to 12000. I will work on your suggestions, but the experimentalists have now told me that they barely had any RNA to begin with, so I assume its really a problem of low quality data. T ...
written 4 months ago by apfelbapfel0
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... Hey Gordon. sorry for the late reply, was traveling. i have to say that this comment of yours confuses me, will i test for DE if using design <- model.matrix(~ y$samples$group)? regarding filtering, library sizes changed for example from 7849976 to 7814960, which I would argue is not much.  ...
written 4 months ago by apfelbapfel0
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... Good points. I am assuming its due to the heterogeneity in the treated individuals, the dont cluster at all. I had run it now in DEseq2, bc I am still learning and thought its good to practice. DEseq2 finds 26 DE genes, how is your experience with regards to trustworthiness of such diverging result ...
written 4 months ago by apfelbapfel0
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... Many thanks to Aaron and Gordon. That mistake with the code was really important to know. Unfortunately still nothing significant to be found, the PI wont be happy. ...
written 4 months ago by apfelbapfel0 • updated 4 months ago by Gordon Smyth37k
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... please just tell me if any further info would be helpful! ...
written 4 months ago by apfelbapfel0
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... The following specs are relevant: After filtering (<1% was removed) group lib.size norm.factors 1 1 7814960 0.9844539 2 1 3638388 0.9664794 3 2 12624890 1.0205424 4 2 10289325 1.0223115 5 1 5545574 0.9718041 6 1 8192437 1.0549536 7 2 4185595 ...
written 4 months ago by apfelbapfel0
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... HI all I am analyzing an RNAseq dataset to find DE genes using edgeR. Strangely I get no significantly differentially expressed genes, and the same FDR for every gene when summarizing the results. I ran the same code on  a public dataset and got fine results, so I guess it has something to do with ...
written 4 months ago by apfelbapfel0 • updated 4 months ago by Gordon Smyth37k
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... Hi there please excuse my very basic questions, but I was not able to find appropriate answers using searchengines. I am trying to analyze a small dataset of the RNAseq of  3 vs 3 samples to identify differentially expressed genes and do some multivariate statistics. Due to the low sample size I c ...
written 4 months ago by apfelbapfel0 • updated 4 months ago by Aaron Lun23k
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... Thanks for the reply. Since i was on a very tight deadline i went with Deseq2 now, but will definitely check out your reply for next time! ...
written 14 months ago by apfelbapfel0
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... Hello After having noticed some spurious results in my data set I wanted to contact this expert community here to get help with choosing the right normalization approach for my data. I have two groups, patients and healthy controls, where microbiota OTUs have been measured from biopsies: Quality f ...
written 14 months ago by apfelbapfel0

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