User: mat149

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mat14920
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Posts by mat149

<prev • 27 results • page 1 of 3 • next >
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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 3 months ago by mat14920 • updated 3 months ago by Aaron Lun16k
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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 7 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 7 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 7 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 7 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 8 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 8 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 8 months ago by mat14920
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ISO help with goana
... Hello, I am running a microarray analysis using a zebrafish platform (pd.zebgene.1.1.st). After performing the moderated t-test in limma (lmFit/eBayes), I am using the resulting MArrayLM object to map the returned Entrez ID's to "dre" (KEGG) and "dr" (GO) databases. I need help with: 1) Restricti ...
limma written 8 months ago by mat14920
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How to filter probesets from the expression set that do not contain Entrez/Gene Symbol identifiers
... Hello,   I am running a limma linear model analysis using expression data produced from affymetrix 1.1 st zebrafish gene arrays.  I am filtering differentially expressed genes between three contrasts and when I call the topTable function, many probesets with NULL/NA identifiers are returned (see b ...
oligo written 8 months ago by mat14920 • updated 8 months ago by James W. MacDonald44k

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