User: mat149

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mat14940
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Posts by mat149

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Comment: C: indexBam(), summarizeOverlaps() error: RNA-seq
... Thank you very much for looking into this and providing these recommendations. To solve this problem, I downloaded the .bam files provided for the updated reference assembly (danRer11 vs. danRer10), and I did not run into any issues. It is likely that the download went awry on the first go Zebraf ...
written 8 weeks ago by mat14940
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Comment: C: Using GenomicFeatures to extract the upstream and downstream region of a transcr
... You can try this, but probably won't work for cds. library(RMariaDB) library(GenomicFeatures) TX<-makeTxDbFromUCSC("name.of.reference.genome.on.UCSC","ensGene") TX xscript<-transcripts(TX) # GRanges for transcripts genes<-genes(TX) # GRanges for genes ...
written 8 weeks ago by mat14940
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indexBam(), summarizeOverlaps() error: RNA-seq
... Hey, I am trying to count the number of reads against genomic features (genes) from an RNA-seq dataset. I downloaded ~100 GB of .bam files that correspond to n=12 samples. I generated index files with 'bamIndex()'. I get an error when trying to make my index files, although the command deposits ...
rsamtools genomicalignments rna-seq written 8 weeks ago by mat14940 • updated 8 weeks ago by Mike Smith3.3k
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Comment: C: How to calculate log2 fold change between two groups in a microarray study
... thank you for your help! My erroneous code was log scaling the values when in fact they were already log transformed exprs(eset['13133579',1:8])->Control exprs(eset['13133579',9:12])->Treat mean(Control)->c mean(Treat)->t log2(t)-log2(c) [1] -0.5313366 ##### ...
written 9 weeks ago by mat14940
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How to calculate log2 fold change between two groups in a microarray study
... Hey, it's a boneheaded question, so please have mercy. How does limma calculate log2 fold change from the matrix of microarray probeset intensities? I am having trouble replicating fold changes of significant genes by hand. These data are from a series of affymetrix single channel microarrays a ...
limma written 9 weeks ago by mat14940 • updated 9 weeks ago by Gordon Smyth37k
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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 14 months ago by mat14940 • updated 14 months ago by James W. MacDonald49k
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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 14 months ago by mat14940
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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 23 months ago by mat14940 • updated 23 months ago by Aaron Lun23k
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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 2.3 years ago by mat14940
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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 2.3 years ago by mat14940

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Popular Question 10 months ago, created a question with more than 1,000 views. For How to select the genes mapped to an enriched KEGG pathway (kegga)

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