User: benjytan1488

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Posts by benjytan1488

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Comment: C: Different results from MDS and PCA plots for DE analysis
... > Second, i don't think you are transforming identical data, at least > from what little R code I can read. There is a rlog function in one > case but not the other, and I wonder if ntop = 1000 means that only > the first 1000 data points are used for PCA. That would definitely > make ...
written 28 days ago by benjytan14880
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Comment: C: Different results from MDS and PCA plots for DE analysis
... > I do not believe that's possible to conclude based on an n of 2 for > each group. Unless the people who did the benchwork can point you to a > clear QC issue, it would be irresponsible to omit any sample. I understand but the sample was prepared and sequenced by a previous member about 3 ...
written 28 days ago by benjytan14880
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Different results from MDS and PCA plots for DE analysis
... Hi all, I have some difficulty understanding my results from DE analysis. Briefly, I have 2 groups (**Dneg** & **Dpos**) with 2 replicates each (total 4 samples). I performed RNA-seq and then used `kallisto` for transcript quantification. I imported the data using `tximport` with the `scaledTP ...
deseq2 pca mds edger written 29 days ago by benjytan14880 • updated 28 days ago by Mensur Dlakic8.1k
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Comment: C: clusterprofiler: Unable to plot results of compareCluster
... I see... I didn't realize there's an "ID" column in the result table which is missing in mine as I used the name "ID' for my data. Thank you very much again for your solution! ...
written 4 months ago by benjytan14880
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Comment: C: clusterprofiler: Unable to plot results of compareCluster
... Thank you very much for the solution. It worked! But I'm curious, why does the "ID" column interfere with the plotting? I don't see any duplicated columns in the data frame... ...
written 4 months ago by benjytan14880
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Comment: C: How to analyze metabolome data?
... I see. If those are derivatives, which values should I use for the analysis? For example, `Glutamine-3TMS` and `Glutamine-4TMS`, how can I combine those results? Or do I have to pick 1 derivative to use? ...
written 4 months ago by benjytan14880
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How to analyze metabolome data?
... Hi, Can anyone please point me to the right direction on how to process my metabolome data? What I received was a Excel spreadsheet as shown below. ![Example Data][1] I tried using MetaboAnalyst and was able to at least analyze the statistical parts. But I was unable to perform enrichment / path ...
metabolomics written 4 months ago by benjytan14880 • updated 4 months ago by Biostar ♦♦ 20
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clusterprofiler: Unable to plot results of compareCluster
... Hi all, I am using the formula interface of `compareCluster` in `clusterprofiler` to look for enriched functional categories in each gene cluster. However, I was unable to plot the results and receive an error message. A reproducible example is shown below. Data table can be downloaded here: https ...
clusterprofiler written 4 months ago by benjytan14880 • updated 4 months ago by huerqiang30

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