User: hesse.sebastian

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Posts by hesse.sebastian

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Interpretation of linear modelling quality test
... I am working with a proteomics dataset and would like to use LIMMA for differential expression analysis. As it was recommended to perform a VOOM transformation I read into the topic and found a way to asses for heteroscedasticity before actually transforming my data without need. I found the lmtest ...
proteomics R statistics written 22 days ago by hesse.sebastian20
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Comment: C: ComBat correction with one batch containing only one sample - keep or remove?
... Thanks, I removed it form the analysis at the end. ...
written 29 days ago by hesse.sebastian20
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Comment: A: LIMMA analysis with 2 samples in comparison group
... Thanks for your comments, unfortunately I am working on a very rare disease (congenital neutropenia) and its feels already quite an accomplishment to have 8 of the disease genotypes in my cohort. So unfortunately I won't get more and there are no other datasets as we are the first performing this ki ...
written 29 days ago by hesse.sebastian20
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LIMMA analysis with 2 samples in comparison group
... In my differential expression analysis dataset (comparing promotes of healthy cells vs diseased cells of patients with defined genotypes) I have a few genotypes with only 2 samples instead of the classically used 3. To give it a try I included them in the makeContrast for LIMMA and it runs without ...
proteomics R limma written 29 days ago by hesse.sebastian20
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Design matrix for voom: with or without batch blocking?
... To calculate differential expression in a proteomics dataset I would like to use LIMMA. I have two questions about it. 1) So far I did the LIMMA analysis on my log2 transformed data only, however it appears that it is recommended to perform a room transformation first as they represent counted data ...
proteomics R limma voom written 29 days ago by hesse.sebastian20 • updated 29 days ago by i.sudbery3.7k
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ComBat correction with one batch containing only one sample - keep or remove?
... I am using sea analysis and combat to correct a proteome dataset. During the correction process ComBat tells me that one batch contains only one sample. Apparently this leads to a modification of the method used: > Note: one batch has only one sample, setting mean.only=TRUE My question is of th ...
proteome sva combat R written 3 months ago by hesse.sebastian20 • updated 26 days ago by Biostar ♦♦ 20
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Comment: C: About BatchQC packages error
... I get the same error! A google search suggested it might be due to missing values (NAs), however I have none. Also used the raw data (instead of log2) and performed a quantile normalization. Also I checked if all samples in the expression matrix are annotated: they are. But still I get the same e ...
written 3 months ago by hesse.sebastian20
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Comment: C: Fold change - a final explanation
... Thanks a lot for your detailed and insightful corrections! ...
written 4 months ago by hesse.sebastian20
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Fold change - a final explanation
... A colleague of mine and I have just been discussing the meaning of fold changes and though this question has been asked before non of the answers are actually as straight forward as needed so lets try here to solve this once and for all. I list here what I understand so far and will update it from ...
rna-seq written 4 months ago by hesse.sebastian20 • updated 4 months ago by jomo018470

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