User: guillepalou4

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guillepalou410
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Posts by guillepalou4

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Comment: C: Can I use Negative Binomial regression to model TPM counts?
... Fine! thank you very much for your help, I really appreciate it :D ...
written 15 days ago by guillepalou410
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Comment: C: Can I use Negative Binomial regression to model TPM counts?
... Ok! Sorry and about the first question of the second offset? ...
written 15 days ago by guillepalou410
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Comment: C: Can I use Negative Binomial regression to model TPM counts?
... Ok I see, thanks. One last thing about this normalization factor (which accounts for library size), I think it would not make much sense in my model, as what I am doing is: NB regression for each **sample** --> gene exp (70.000 transcripts) ~ variable_interest + offset(log(transcript_leng ...
written 16 days ago by guillepalou410
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Comment: C: Can I use Negative Binomial regression to model TPM counts?
... I thought you should not use VST on the TPMs. So my two alternatives would be: 1) NB with raw counts + offset of gene length 2) NB? with VST on TPM counts ...
written 16 days ago by guillepalou410
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Comment: C: Can I use Negative Binomial regression to model TPM counts?
... Hi i.sudbery, thanks. Do you mean using VST normalization into the raw counts data (not TPM) and then using the NB regression? ...
written 19 days ago by guillepalou410
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Comment: C: Can I use Negative Binomial regression to model TPM counts?
... Hi dariober, thanks for the answer. I was thinking on this alternative method you mentioned, but using gene length as an offset (not as a covariate). I have read other people using this https://www.biostars.org/p/368862/ > "Another alternative would be to use negative binomial regression, but &g ...
written 19 days ago by guillepalou410 • updated 19 days ago by ATpoint41k
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Can I use Negative Binomial regression to model TPM counts?
... Hi, The question is simple. Can I use a Negative Binomial regression to model Transcripts Per Million (TPM) as the outcome/response variable? It is usually used on raw count data, but I am interested in TPM, as I need to normalize for gene length (but not interested in DE analysis). Thank you Gui ...
tpm negative binomial rna-seq written 20 days ago by guillepalou410 • updated 20 days ago by dariober11k
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Comparison of ratio of expression between two genes across samples
... Hi guys, I have been reading a lot about within-sample and between-sample RNA-seq normalization but I still haven't found an answer for my question. My data consists of an RNA-seq matrix with Transcripts-Per-Million (TPM) values, so it is within-sample normalized. I want to compare the expression ...
normalization tpm relative abundance rna-seq written 25 days ago by guillepalou410
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Correcting RNA-seq matrix by removing principal components gives negative values in the matrix
... Hi guys, I have an RNA-seq matrix with Transcripts-Per-Million (TPM) values on the cells. It contains 87 samples and 25307 transcripts (after removing 0 counts and low-expressed genes). Values ranges from 0 to 77499.55. I wanted to perform a PCA and remove the first 4 principal components to corre ...
principal components tpm rna-seq pca written 26 days ago by guillepalou410
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Comment: C: TCGAbiolink does not download all the data requested
... Hi Kevin, thanks for the answer, I finally solved it. It is true that the 11 files contain RNA-seq FPKM-UQ files but although I used a "Solid normal tissue" filter, those files were from primary tumors. Weird. But at least the downloads are correct. About the last comment... Which type of analyses t ...
written 9 weeks ago by guillepalou410

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