User: John

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John0
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Posts by John

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Limma, remove batch effects and technical replicates
... Hello Aaron, Thank you for a very quick answer and good explanation to quench curiosity, which I can understand. Yes, I understand it is not a good thing, as I stated too. As for your technical replicate question, yes and no. What I mean is, the technical replicates for each bio replicate have the ...
written 2.6 years ago by John0
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Comment: C: Correcting for known and surrogate variables in DESeq2
... Hello Bernd, Thank you very much for your help and advice, for a comprehensive answer, very helpful. The publications also great. For random interest, I have also noticed the Limma removeBatchEffect function in addition to SVA and RUV, which seems to work pretty well on my data.  best,  John.   ...
written 2.6 years ago by John0
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Limma, remove batch effects and technical replicates
... Hello.  I have data that has 2 treatment groups (6 samples, 3 bio reps each group). For each bio rep, I have 9 technical reps, so 54 total samples. I have a co-variate of number of mutations and a date of experiment of batch effect. The size of the gene expression matrix = 5000 genes by 54 samples. ...
limma duplicatecorrelation removebatcheffect() written 2.6 years ago by John0
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Comment: C: Correcting for known and surrogate variables in DESeq2
... Dear Bernd, Thanks for an interesting post and a useful answer to it. This extraction of frozen data has helped me. I also view PCA of data with batches removed. Great, it seems from PCA that SVA is working very well.  Please can you explain this comment?  PS: Do not use the cleaned data for dow ...
written 2.6 years ago by John0
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Comment: C: Limma; design matrix for treatments and sibship
... Thanks Gavin for the clear logic in your answer and a solution, that helps a lot.  John. ...
written 3.6 years ago by John0
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Comment: C: Limma; design matrix for treatments and sibship
... Thanks for the answer and code. I understand this is similar to section 9.4.1 of the Limma manual. I thought the empty vector is related to the geneInsert samples, as that same vector is used in both sample groups; 1) to insert the gene and 2) the vector alone without the gene insert. Some genes wi ...
written 3.6 years ago by John0
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Answer: A: Limma; design matrix for treatments and sibship
... Added as a comment.  ...
written 3.6 years ago by John0
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Limma; design matrix for treatments and sibship
... Hello. I have a targets file as follows;               treat sibship file1   GeneInsert   1 file2   GeneInsert   2 file4  EmptyVector   1 file5  EmptyVector   2 file7 no_treatment   1 file8 no_treatment   2 Treat = treatment by tranfsection of an interesting gene, or with an empty vector transfec ...
limma design and contrast matrix written 3.6 years ago by John0
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Answer: A: edgeR and Normalization of RNAseq data using ERCC controls
... Dear James and Ryan, That information is interesting and very helpful, thank you.  John. ...
written 4.5 years ago by John0
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edgeR and Normalization of RNAseq data using ERCC controls
... Dear List, I have read a useful segment from a BioStar post on using DESeq with ERCC controls to normalize RNAseq counts.  Contained on the page (https://www.biostars.org/p/81803/), is the statement; "Read in the count data, subset the resulting matrix such that it includes only the spike-ins, cr ...
edger ercc written 4.5 years ago by John0

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Popular Question 3.5 years ago, created a question with more than 1,000 views. For edgeR and Normalization of RNAseq data using ERCC controls

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