User: John
John • 0
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Posts by John
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... 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 2.4 years ago by
John • 0
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... 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.
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written 2.4 years ago by
John • 0
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... 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. ...
written 2.4 years ago by
John • 0
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... 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 2.4 years ago by
John • 0
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... Thanks Gavin for the clear logic in your answer and a solution, that helps a lot.
John.
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written 3.4 years ago by
John • 0
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... 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 3.4 years ago by
John • 0
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... 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 ...
written 3.4 years ago by
John • 0
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... Dear James and Ryan,
That information is interesting and very helpful, thank you.
John.
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written 4.3 years ago by
John • 0
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... 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 ...
written 4.3 years ago by
John • 0
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3.3 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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