User: lirongrossmann

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Posts by lirongrossmann

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Alternative splicing with covariates
... Thanks, Kevin! I actually got a file of samples with PSI values for each splicing events that was generated by a yet unpublished method and want to see if there is a statistical difference between the PSI values between two groups within the dataset. Does DEXseq work with PSI values? ...
written 8 days ago by lirongrossmann20
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Alternative splicing with covariates
... Hi everyone, I have a file containing psi values for samples and I wanted to compare the differential splicing between two groups of my datasets, adjusting for covariates. Can I just give the dataset of the splicing events to limma? Is there a statistic method especially designed for that kind of da ...
splicing limma rna-seq written 8 days ago by lirongrossmann20 • updated 8 days ago by Kevin Blighe3.2k
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Comment: C: Selecting genes that best separate between two groups
... Thanks! I'm now stuck with another related problem on a different dataset. I run Deseq2 on the dataset, I get a handful of DE genes between two groups of interests in my dataset. I run pca on the expression matrix with only the DE genes selected, and I don't see the two groups separating. How ca ...
written 22 days ago by lirongrossmann20
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Comment: C: Selecting genes that best separate between two groups
... Did you use the LDA on the log transformed expression matrix? ...
written 25 days ago by lirongrossmann20
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Comment: C: Strand specific and unstranded dataset
... Thanks! What I am a little confused about is that rld is obtained using the model with batch as a confounder for the differential expression but it does not remove the batch, so how can I tell that the batch was removed? (btw, it's a different data set from the one we are talking about in the other ...
written 25 days ago by lirongrossmann20 • updated 25 days ago by genomax34k
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Comment: C: Selecting genes that best separate between two groups
... Thank you for the code! Is it supposed to be project.pca <- prcomp(assay(vsd))? The column in my vsd are the samples and the row are the genes. If I go by t(assay(vsd)) I got PCA for the samples rather than the genes. ...
written 25 days ago by lirongrossmann20
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Comment: C: Different PCA plots using rlog and vsd on the same data set
... Thank you! I have been using variance-stabilised transformation mainly because rlog runs very slowly. In your experience, does rlog give better results? ...
written 25 days ago by lirongrossmann20
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Comment: C: Selecting genes that best separate between two groups
... Thank you so much for your help! They don't cluster so nicely in the dendogram. I'll try to describe in more detail what I did: I created a Deseq2 object using my raw count matrix and metadata. I then applied variance stabilization transformation on the data and plot PCA. I see two distinct groups ...
written 25 days ago by lirongrossmann20
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Comment: C: Different PCA plots using rlog and vsd on the same data set
... I would love to! Is there a way to upload the plots? ...
written 26 days ago by lirongrossmann20
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Comment: C: Selecting genes that best separate between two groups
... I initially wrote my response as a comment but was asked to write it as a reply to your comment. Sorry for the confusion. When I look at my data using PCA the variance explained by PC1 is 14% and 10% by PC2. I know the samples are biologically different regardless of my grouping as some of them have ...
written 26 days ago by lirongrossmann20

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