User: mat149

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mat14920
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Posts by mat149

<prev • 29 results • page 1 of 3 • next >
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Making microarray probeset presence/absence calls
... Hello, I have an inquiry on how to apply the "paCalls" function of the oligo package.  I received a wicked error message after running the "paCalls(CELdat, "PSDABG")" line which states:  Computing DABG calls... Error in 0:max(counts) : result would be too long a vector In addition: Warning message ...
oligo written 8 weeks ago by mat14920 • updated 8 weeks ago by James W. MacDonald46k
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Answer: A: Converting gene symbol list to Entrez IDs
... Here is a code chunk that I use to convert zebrafish gene symbols to Entrez gene ID's: ("t" in this case is of class character with random genes that I'm interested in, but you can use your "read.csv" object) library(org.Dr.eg.db) keytypes(org.Dr.eg.db) library(clusterProfiler) t <- c("lepa", ...
written 8 weeks ago by mat14920
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Help: extract counts from RNA-seq .bam/.bai files
... Hello, I have an inquiry on a paired-end RNA-seq experiment prepared from zebrafish livers.  I would like to identify differentially expressed transcripts (or genes) between (n = 5) "control" and (n = 5) "lepa" samples. I am looking for a method that will construct a matrix of counts from (n = 10) ...
edger counts written 11 months ago by mat14920 • updated 11 months ago by Aaron Lun19k
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Answer: A: Duplicate gene ID's returned from limma microarray analysis
... Thank you for your comment, James. I have implemented both getMainProbes and Gordon's suggested code into my analysis and it has really helped to "clean up" my dataset. Problem solved! ...
written 15 months ago by mat14920
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Comment: C: Duplicate gene ID's returned from limma microarray analysis
... Thank you for your insight. It is an Affymetrix 1.1st zebrafish gene array strip.  I wrote the toptable out to an .xlsx and sorted them alphabetically, then copied/pasted the first few probesets just for illustration purposes.     edit: I processed the dataset with RMA ("core") and derived annot ...
written 15 months ago by mat14920
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Duplicate gene ID's returned from limma microarray analysis
... Hello,   I am using the limma package to detect differentially expressed probesets between three groups of samples (knockdown, rescue, and control). When I pass my topTable arguement, probesets with the same gene symbol identifier are returned which also have (near) identical fold changes + p.valu ...
microarray limma written 15 months ago by mat14920
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Comment: A: Probe sequences to Entrez Ids
... hey theobroma22, can you provide the name of the array platform that you are using? if it is Affymetrix, try 'affycoretools' ...
written 15 months ago by mat14920
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Comment: A: ISO help with goana
... Thank you, Gordon.  With your help, I figured out How to determine which genes are assigned to each enriched GO term.  I will do some reading regarding the comments/links you posted and try to determine which method might be best for my dataset ...
written 16 months ago by mat14920
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Comment: C: ISO help with goana
... sorry, I was not paying attention and posted the kegg script by accident. entzzvec<-as.vector(data.fit.eb$genes$ENTREZID) MOgo <- goana(data.fit.eb, coef=1,FDR=0.01,geneid=data.fit.eb$genes$ENTREZID,species="Dr") topMOgo<-topGO(MOgo,number=50) I had to use the as.vector step to map gene ...
written 16 months ago by mat14920
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Comment: C: How to filter probesets from the expression set that do not contain Entrez/Gene
... Thanks, Gordon, this code worked for removing the N/A's as i hoped.  I am still considering removing duplicate identifiers... but I am uncertain how removing duplicate Symbol/Entrez ID's may influence the analysis. ...
written 16 months ago by mat14920

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