User: Alexander Az.

gravatar for Alexander Az.
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New User
Location:
Armenia
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1 day, 12 hours ago
Joined:
1 year, 1 month ago
Email:
a*******@gmail.com

Posts by Alexander Az.

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Comment: C: Subsetting a data frame generated by topTable() {limma}
... PS: It is now a matter of giving wrong naming in the abs( ) function. The underscore is just a typo in this section ...
written 6 days ago by Alexander Az.10
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Subsetting a data frame generated by topTable() {limma}
... I am trying to set certain criteria of choice for picking DE genes, after using limma workflow. I want to select genes that have adjusted p-value < 0.05 and absolute value of log2 fold change > 0.5. The code I used is: ``` significant <- topTable_result[which(topTable_result$adj.P.Val<0 ...
microarray limma toptable written 6 days ago by Alexander Az.10 • updated 6 days ago by Gordon Smyth38k
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Comment: C: AnnotationData Packages for Agilent microarrays
... James I really need to thank you for your imediate response. You have been really helpfull. I still need to have some genes annotated with ENTREZ Gene ID or Unigene, not just ENSEMBLE IDs. I shall find a way to make this correspondance. Thank you again ...
written 9 days ago by Alexander Az.10
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AnnotationData Packages for Agilent microarrays
... I am using Agilent's Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Probe Name Version) (GPL14550), Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version) (GPL4133) and Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Feature Number version) (GPL16 ...
microarray annotation limma agilent .db written 9 days ago by Alexander Az.10 • updated 9 days ago by James W. MacDonald51k
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Visualization of analysis of multiple cell lines
... I have a certain EList containing data for three cell lines. I need to plot MDS plots for each one of them separately. Are there any ideas of how can this be feasible? plotMDS(EList$E, ...) would plot an MDS for all 3 cell lines. How can I visualise each one seperately? Thanks in advance, Alexan ...
limma plotmds cell lines written 12 months ago by Alexander Az.10 • updated 12 months ago by Gordon Smyth38k
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Comment: C: Trouble loading 'lumi' package
... Hello Lei, Thank you fo your instant reply. Unfortunately the trouble proved to be more persistant. Issue has occured right after upgrading to R v.3.5.1, ergo I assume I have to address to the authors of 'lumi' for an immediate mend. Best regards, Alexander ...
written 13 months ago by Alexander Az.10
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Trouble loading 'lumi' package
... Recently I've been having hard times trying to load the 'lumi' package. The message I am receiving is:  Error: package or namespace load failed for ‘lumi’:  .onLoad failed in loadNamespace() for 'HDF5Array', details:   call: init_global_counter(filepath)   error: file 'C:\Users\EE49~1\AppData\Lo ...
lumi illumina hdf5array written 13 months ago by Alexander Az.10 • updated 13 months ago by James W. MacDonald51k

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