User: goldie.ed

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goldie.ed10
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Posts by goldie.ed

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Average dataframe columns according to a corresponding vector.
... I was able to change the vector elements to represent a pattern within the column names and thus was able to use your suggested solution. Still - I wonder if there is another way in situations when the elements does not share a similar patterns. ...
written 5 days ago by goldie.ed10
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Comment: C: Average daraframe columns according to a corresponding vector.
... This wont work for me - the vector does not correspond to the column names. ...
written 5 days ago by goldie.ed10
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Comment: C: Average daraframe columns according to a corresponding vector.
... Thank you very much the thing is - the number is the patient number - and the data contains about 40 patients. I want to average each of them. just to be clear - patient has 3 conditions - Lm, SL , control. and i would like to average all his control samples together... and to do this for all pati ...
written 5 days ago by goldie.ed10
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Average dataframe columns according to a corresponding vector.
... I have gene expression data frame: ![df example](https://i.ibb.co/HKLZmth/Capture.png) and i have a vector which correspond to the columns: ![vector](https://i.ibb.co/LRcYGCR/Capture.png) I would like to average the mean of the same columns according to the vector. so the two first two "Lm 10" col ...
R written 5 days ago by goldie.ed10 • updated 5 days ago by ATpoint17k
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Comment: C: Batch effect correction
... Hi, I did not understand what do you mean by incorporate new design into DESeq2 after I removed the batch effect. Can I use the new batch corrected matrix as input for DESeq2? from what I read DESeq2 input can be only original count matrix and it cannot be given log-transformed matrix. Is it valid ...
written 14 days ago by goldie.ed10
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Comment: A: Batch effect correction
... Thank you very much guys you have been a great help. One more question - I heard loess normalization can also be used for dealing with batch effect. Can it be used in my situation? thanks ...
written 18 days ago by goldie.ed10
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Comment: A: Batch effect correction
... Thank you very much for your detailed answer. After posting this question I figured a way to remove the batch effect but I wonder whether what I did is valid. I would be happy to get your opinion. I separated each condition from all plates and than I used limma's function to remove the batch effect ...
written 19 days ago by goldie.ed10 • updated 19 days ago by genomax68k
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Batch effect correction
... Hello, I'm very new to rna-seq analysis and I would love to get some help regarding batch effect in my data. Data is comprised of 40 individuals (blood samples) 3 conditions (control, infection 1, infection 2. each individual has 3 replicates for each conditions- overall 120 *3 samples) the prep ...
rna-seq written 20 days ago by goldie.ed10

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