User: reubenmcgregor88

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Posts by reubenmcgregor88

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Comment: C: Microarray analysis in R (Limma): how to select genes exclusively expressed in o
... Thank you Friederike, could you please expand on this. Using your example I would like to select (for instance), row 2 based on a)it has NA in columns b and c, b) it has a non-NA in column a. Using the "subset" above I could specific which rows to pull out based on NA but not which rows to pull o ...
written 11 days ago by reubenmcgregor8840
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Comment: C: Microarray analysis in R (Limma): how to select genes exclusively expressed in o
... I understand, I guess this is more of a coding question. I am not sure what is wrong with the data, but it seems to be working fine in this case. This is the only format I can get the data in for the moment. I will look into getting the data further upstream so I can QC it. ...
written 11 days ago by reubenmcgregor8840
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Microarray analysis in R (Limma): how to select genes exclusively expressed in one condition.
... Background: I am mining some data using the Limma package to look at differentially expressed genes. I have imported the expression data such that values of 0 are NA. y <- read_excel("exprs.xlsx", na="0") My phenotypic data looks like this: > pData tissue donor ...
R microarray limma written 12 days ago by reubenmcgregor8840 • updated 11 days ago by h.mon24k
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Comment: C: Array Normalization on focussed array in Limma using R
... Yes happy with Gordons response, I guess would be good for others to see his answer too. ...
written 10 weeks ago by reubenmcgregor8840
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Comment: C: Array Normalization on focussed array in Limma using R
... Yes it has, sorry did not realise it was forwned upon I will delete post here as it was answered there ...
written 10 weeks ago by reubenmcgregor8840
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Comment: C: Array Normalization on focussed array in Limma using R
... Thanks I will try that, although reading the Vignette this will not solve the problem of few proteins which we have chosen specifically due to their high variance between cases and controls? ...
written 10 weeks ago by reubenmcgregor8840
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Comment: C: Array Normalization on focussed array in Limma using R
... Thanks Kevin, point taken, I have updated the post. As many posts on here I have come to the project late and do not have all of the information about what analysis was done etc, and we have asked but they are asking to charge us extra for more "bioinformatics services". As mentioned above I have al ...
written 10 weeks ago by reubenmcgregor8840
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(Closed) Array Normalization on focussed array in Limma using R
... I have been analysing protein array data with hundreds and thousands of proteins using Limma in R. For normalisation I have been using the following: y <- normalizeBetweenArrays(log2(exprs), method="quantile") followed by box plots and density plots for QC. Followed by linear model fittin ...
array R limma written 10 weeks ago by reubenmcgregor8840
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What values should I use for principle component analysis of microarray data?
... I have been doing a bit of reading about Principle Component Analysis (PCA) and have been using R to carry out PCA on some microarray data and have started with background subtracted raw fluorescent values. I can run PCA on any of the following datasets, each one giving different plots: 1) Unnorma ...
R pca microarray written 7 months ago by reubenmcgregor8840 • updated 7 months ago by Kevin Blighe39k
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Comment: C: What files should I ask for from protein array analysis, in order to carry out d
... Thanks, yes it will be more or less indistinguishable from microarray in many ways. Given that, my question is in order to import and use in Limma what should I ask for.My question is more about the terminology of what to ask for. I do not want to have to go through the normal QC and background su ...
written 8 months ago by reubenmcgregor8840

Latest awards to reubenmcgregor88

Popular Question 9 weeks ago, created a question with more than 1,000 views. For annotatePeaks.pl Homer using "RNA"
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Popular Question 13 months ago, created a question with more than 1,000 views. For ggplot2, point with border

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