User: lirongrossmann

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Posts by lirongrossmann

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Genes for clustering
... The data is rna-seq. There were too many genes and the program is still running. It runs nicely with fewer genes (I have 30,000) Thanks ...
written 5 weeks ago by lirongrossmann20
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Genes for clustering
... Hi everyone, I have a group of samples which is supposed to be biologically homogeneous. I want to cluster the genes to see which are highly expressed and which are lowly expressed across all samples. I tried hierarchal clustering but it got stuck because there are so many genes. I don’t want to us ...
hierarchical clustering clustering written 5 weeks ago by lirongrossmann20
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Comment: C: Converting unstranded samples to strand specific
... Thank you for the detailed answer. I agree with your comments. I may not have been explicitly clear about what I would like to achieve from the conversion. I built a model to predict groups based on their gene expression using the stran specific samples. I want to verify my model using the unstrande ...
written 7 weeks ago by lirongrossmann20
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Comment: C: Converting unstranded samples to strand specific
... Will you please be able to briefly explain me why? ...
written 7 weeks ago by lirongrossmann20
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Converting unstranded samples to strand specific
... Hi All, I have a two datasets of rna-seq samples, one consists of strand-specific protocol (Truseq) and the other one unstranded (Clontech’s SMART). I would like to use both datasets (to increase the power of my study) and tried batch effect correction, but it did not go well (I still see two clear ...
rna-seq strand written 7 weeks ago by lirongrossmann20 • updated 7 weeks ago by Friederike890
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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 I actually got a file of samples with PSI values for each splicing events that was generated by a yet unpublished method and want to see if there is a statistical difference between the PSI values between two groups within the dataset.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 9 weeks 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 9 weeks ago by lirongrossmann20 • updated 9 weeks ago by Kevin Blighe9.3k
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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 11 weeks 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 11 weeks 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 11 weeks ago by lirongrossmann20 • updated 11 weeks ago by genomax39k

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