User: alakatos

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alakatos80
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Posts by alakatos

<prev • 69 results • page 1 of 7 • next >
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Tools for classifying reads from xenograft samples?
... Hello All,  I must separate human and mouse RNAs obtained by RNAseq from a tissue after xenotransplantation (human NSCs to mouse model).  Would you please suggest Bioconductor or other tools for classifying reads from xenograft samples? What is the recommended read depth and length for this kind o ...
rnaseq xenograph written 3 months ago by alakatos80
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Comment: C: Filtering DGEList object in edgeR
... Thank you. A   ...
written 4 months ago by alakatos80
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Comment: C: Filtering DGEList object in edgeR
... It worked. Thanks. ...
written 4 months ago by alakatos80
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Filtering DGEList object in edgeR
... Hello All,  I made a DGEList object. d <- DGEList(counts = COUNTS[,8:43], group = condition,genes=COUNTS$HGNC_symbol)   I added  additional parameters to the list. rownames(d) <- COUNTS$Ensembl d$ENTREZ <- COUNTS$NCBI_geneID d$ENSEMBL <- COUNTS$Ensembl d$Symbol <- COUNTS$HGNC_ ...
edger filter dgelist written 4 months ago by alakatos80 • updated 4 months ago by Gordon Smyth32k
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Comment: C: RNAseq with technical replicates: Does it sound right?
... Hi Ryan, Thanks for your reply.  I would like to clarify it further. Are you suggesting that having many files with lower counts as technical replicates and then combining them (adding up the raw counts of  3 files)  is a  better way to go than having one  file with  ~ 30 million reads. Along thos ...
written 5 months ago by alakatos80
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RNAseq with technical replicates: Does it sound right?
... Dear All,  I processed and analyzed RNAseq data before. It was pretty straight forward with Star, featureCounts and edgeR. I received a new dataset of  36 samples with SE sequence file. I expected 36 files with ~30 million reads. Instead, I got 108 files (18 samples/per lanes with ~ 10 million rea ...
rnaseq edger technical replicates written 5 months ago by alakatos80 • updated 5 months ago by Ryan C. Thompson6.1k
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Comment: C: RNAseq read coverage plot: What tool?
... Thank you all for your help. Anita   ...
written 7 months ago by alakatos80
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RNAseq read coverage plot: What tool?
... Hello All,  I would like to generate a similar RNAseq read coverage plot  (attached) of a gene  for multiple samples (12).  Would you please recommend a tool in Bioconductor?     http://imgur.com/bpxTOow Thanks  a lot, Anita ...
rnaseq visualization plotcoveragehist written 7 months ago by alakatos80 • updated 7 months ago by Ou, Jianhong1000
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Comment: C: How to transform edgeR output into a cummeRbund object?
... Hi James,  Thank you for your answer.  Anita  ...
written 7 months ago by alakatos80
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How to transform edgeR output into a cummeRbund object?
... Hi All,  I analyzed my data RNAseq data with edgeR but I like the ease of visualization by cummeRbund. I was wondering if there is a way to transform "fit output" and  the "normalized counts" of edgeR to cummeRbund object. I tried but I could not make it work. Any suggestions are welcomed! Than ...
edger cummerbund written 7 months ago by alakatos80

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Popular Question 7 months ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 19 months ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 19 months ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays

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