User: juls

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juls0
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Posts by juls

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ReactomePA enrichMap function - a question regarding the connections between nodes
... Dear all, Using the ReactomePA package I have visualised the enrichment results by means of the enrichMap function (for an example see the original publication, Figure 1 http://pubs.rsc.org/en/content/articlepdf/2016/mb/c5mb00663e). I am wondering though what the connections between the nodes mean ...
reactomepa written 4 months ago by juls0 • updated 4 months ago by Lluís R300
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Comment: C: ReactomePA gsePathway - a couple of questions regarding the input and output
... Thank you for your answer! ...
written 7 months ago by juls0
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Comment: C: ReactomePA gsePathway - a couple of questions regarding the input and output
... I am sorry - I am not sure I understand correctly. So you are saying I can use both - fold changes as well as log2 fold changes in the gsePathway function - and the results are different due to the way they are used in the calculations?      ...
written 7 months ago by juls0
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Comment: C: ReactomePA gsePathway - a couple of questions regarding the input and output
... Thank you for your quick reply. Just one more follow-up question - why are the results different? ...
written 7 months ago by juls0
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Comment: C: ReactomePA gsePathway - a couple of questions regarding the input and output
... Thanks for the link. I briefly read the paper related Bioconductor package (http://pubs.rsc.org/en/content/articlepdf/2016/mb/c5mb00663e) and couldn't find it.  Relating to the second question: do you mean I can use both? Either FC or log2FC? The results are different.      ...
written 7 months ago by juls0
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ReactomePA gsePathway - a couple of questions regarding the input and output
... Dear all, I have a couple of questions regarding the input and output of the gsePathway function:  1) In the resulting data frame - what is NES, core enrichment and what is the rank? 2) Should I use the fold changes or the log2FC in the gsePathway function? Thank you very much for your help! Bes ...
reactomepa written 7 months ago by juls0
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Comment: C: Adjust for multiple batches using combat
... Thanks again! It was suggested previously as a solution to Combat not being able to handle multiple batches, but I did not feel very confident about it.    ...
written 8 months ago by juls0
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Comment: C: Adjust for multiple batches using combat
... Thank you very much for your answer! Very helpful! I have done something similar to what you described.  Combat cannot take multiple batched at the same time - so I used it sequentially giving it a batch to correct for and a design matrix with my interesting factor plus covariates (uninteresting fac ...
written 8 months ago by juls0
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Adjust for multiple batches using combat
... Dear all, I have patient data (microarray data > 100 samples, very noisy) - and as always there are many factors (disease/control, infection, age, sex, treatment, cohort, pmi, batch/scandate).  So my question is basically a generell question concerning combat. I am interested in two biological ...
limma sva combat written 8 months ago by juls0 • updated 8 months ago by Aaron Lun17k
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Comment: C: Cutoff for coexpressed gene pairs using Pearson/Spearman correlation
... Thanks for your answer. I adjusted the p value, so it's around 0.18 but yes it's very low. Hence my question about an "established" cutoff. Any suggestions about a sensible cutoff here? (The above list was also meant for negative correlation of course. I classified with the abs(correlation). I thou ...
written 8 months ago by juls0

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