User: reubenmcgregor88

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Posts by reubenmcgregor88

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Comment: C: Am I on the right tracks with a 3 factor design in Limma?
... Ok, understood I will look into Limmas normalisation procedures and QC etc and do it from there and then compare to the  "who-knows-what company. Always good to check I guess.  Thank you for all the help ...
written 16 days ago by reubenmcgregor880
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Comment: C: Am I on the right tracks with a 3 factor design in Limma?
... Thanks. I see there is something I am not quite understanding. I am trying to understand the analysis in term of my experience with another package on RNAseq data where un-notmalised data is put in and normalised data is output by the model. I have asked for the raw expression, normalised values fro ...
written 16 days ago by reubenmcgregor880
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Comment: C: Am I on the right tracks with a 3 factor design in Limma?
... I feel like I will be apologising allot if I'm not careful, I will be next time, sorry. I changed all me phenotypic data half way through writing the post as I realised some of my nomenclature was too long winded so I originally had control_NA which I replaced with na, I have updated the post to r ...
written 16 days ago by reubenmcgregor880
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Comment: C: Am I on the right tracks with a 3 factor design in Limma?
... Whoops, miss read your comment again sorry, yes sure: output of original data: > summary( apply(exprs,2,min) )    Min. 1st Qu.  Median    Mean 3rd Qu.    Max.      5.0    60.0   101.0   127.9   165.0   716.0 Same but with log2 transformed values: > summary( apply(exprs,2,min) )    Min. 1st ...
written 16 days ago by reubenmcgregor880
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Comment: C: Am I on the right tracks with a 3 factor design in Limma?
... Thanks Gordon, Sorry I should have clarified I am not using the right data. I am using the raw values to get my head around the structures etc in Lima. I have edited the post to highlight this.  ...
written 16 days ago by reubenmcgregor880
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Am I on the right tracks with a 3 factor design in Limma?
... IMPORTANT: I am using a "dummy" dataset to just get my working right and get used to Limma workflows, as pointed out the values are raw fluorescence value while I await the appropriate transformed expression data. The "real" data will come in the same txt format but with the normalised and transform ...
biobase limma R design matrix written 16 days ago by reubenmcgregor880 • updated 16 days ago by Gordon Smyth34k
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Comment: C: Have I used Deseq2 ,on protein array data, correctly? Or should I be using anoth
... Thank you, I assumed if I had some kind of data that was equivalent to “counts” I.e background subtracted and corrected data, so essentially have protein abundance data, that the analysis would be equivalent. Showing my ignorance I guess. ...
written 18 days ago by reubenmcgregor880
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Have I used Deseq2 ,on protein array data, correctly? Or should I be using another R package
... We had some protein microarrays done I believe using the hu-prot platform. I asked for non-normalised corrected data hoping to run in DeSeq2 (as I have used this for RNAeq data before). The count data imported as "cts" looks something like this:   RF0064 RF0065 RF0070 CO ...
deseq2 R protein microarray written 18 days ago by reubenmcgregor880 • updated 18 days ago by Gordon Smyth34k
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Comment: C: How to get sequence homology percent from a multiple sequence alignment in DECIP
... Ah ok, I will go back to reference material and try and understand more,  Thanks ...
written 11 weeks ago by reubenmcgregor880
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Comment: C: How to get sequence homology percent from a multiple sequence alignment in DECIP
... If the distance Matrix looks like this:  BOD1L2    BOD1L1      BOD1  0.8895349 0.9459459 0.0000000  Does that mean BOD1L1 is 94% homologous to BOD1 and BOD1L2 is 88% homologous to BOD1? Or something similar? Sorry for simplicity of questions   ...
written 11 weeks ago by reubenmcgregor880

Latest awards to reubenmcgregor88

Scholar 11 months ago, created an answer that has been accepted. For A: Error in pcaplot3d from pcaExplorer, when running Deseq2 since update of package

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