User: carl.h

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carl.h10
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Posts by carl.h

<prev • 20 results • page 1 of 2 • next >
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Comment: A: Suggestions on open databases
... I am interested in humans to be able to study the correlations of specific genes in different clinical settings. ...
written 2.8 years ago by carl.h10
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Suggestions on open databases
... Does anybody have any suggestions on publically open data bases with gene expression, copy number or snp data that is worth mining? Preferably with clinical data. TCGA is of course one of those, but I was wondering if anyone has experience with others? ...
rna-seq written 2.8 years ago by carl.h10
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Comment: C: How to compare correlations between tumor samples
... Thank you for your input, it helps me get to the bottom of this. I agree it is not strange that many genes are correlated with eachother, in these cases - thousands of them - but then the question comes how much is just by chance if a certain amount of all genes is correlated with eachother. And bet ...
written 3.6 years ago by carl.h10
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Comment: C: How to compare correlations between tumor samples
... Thank you for your answer! What do you make of this? I have done a correlation with the GOI to the other gens, which I plotted on the x-axis. The blue is with p-value<0.05. The dot names is for each individual Cancer. So from this image it seems to be some genes that would have higher correlatio ...
written 3.6 years ago by carl.h10
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Comment: C: How to compare correlations between tumor samples
... I posted reply above. ...
written 3.6 years ago by carl.h10
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Comment: C: How to compare correlations between tumor samples
... Thank you for the answer. Yes, so to be more precise. I am correlating normalized gene expression data. So the gene expression data of one gene compared to 20 other genes in each cancer. In the TCGA database there are something like 30 kinds of cancers with very varying sample sizes (but in total l ...
written 3.6 years ago by carl.h10
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How to compare correlations between tumor samples
... I would like to compare the correlation of a set of genes to a certain gene of interest (GOI) and compare these between different gene sets. I know from before that these genes have correlation to the GOI in protein assays, but I would like to use the TCGA data to confirm this in multiple tumors. ...
rna-seq written 3.6 years ago by carl.h10 • updated 3.6 years ago by DG7.1k
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How do I set up the contrast of these variables?
... I am trying to wrap my head around how the model matrix works and how to use it to analyze data. I have a model analyzing rna seq data where I have 2 genotypes I want to compare in different conditions and overall. The samples are either KO or WT genotypes. I have 2 treatments treated and untreate ...
rna-seq written 3.6 years ago by carl.h10 • updated 3.6 years ago by theobroma221.1k
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Comment: C: How to visualize gene difference with PCA?
... No I have not corrected for batch effect. I have 4 biological replicates which I guess could be corrected, because they cluster slightly more than other parameters. The groups I am talking about is for example all samples at one timepoint cluster in one area and the other timepoint in the other. ...
written 3.7 years ago by carl.h10
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Comment: C: How to visualize gene difference with PCA?
... I can color the points to each sample if they have different timepoints and so on by adding different designs. But I don't know how I would do that to different genes which are expressed by several samples. ...
written 3.7 years ago by carl.h10

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