User: alakatos

gravatar for alakatos
alakatos100
Reputation:
100
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Trusted
Location:
United States
Last seen:
1 year, 5 months ago
Joined:
4 years, 8 months ago
Email:
a*******@uci.edu

Posts by alakatos

<prev • 73 results • page 1 of 8 • next >
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Answer: A: Is Limma's removeBatchEffect() and log2() commutative?
... Aaron,  ​I tried your example code at  and recevied an error message. (I changed desing to design.all) pseudo.counts <- q2qnbinom(y$counts, old.fitted, new.fitted, dispersion=0.05) Error in raw.mat[i, , drop = FALSE] : (subscript) logical subscript too long I am not sure what I was doin w ...
written 18 months ago by alakatos100
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Comment: C: edgeR:fitted and partial expression values
... "Are you saying you want to regress out particular covariates and use the corrected observations for downstream analyses?" Yes. Thanks Aaron very much. It is very helpful. ...
written 18 months ago by alakatos100
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edgeR:fitted and partial expression values
... Hello Everyone, I have a very noise RNAseq dataset with several covariates analyzed in edgeR. design <- model.matrix(~0 + conditions + cov1 + cov2, data=pheno) d <- calcNormFactors(d, method ="TMM") d <- estimateDisp(d, design, robust=TRUE ) fit <- glmFit(d, design, dispersion=d$trend ...
edger cpm explained variance fitted model written 18 months ago by alakatos100 • updated 18 months ago by Gordon Smyth37k
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Incorporating 'offset' into edgeR pipeline
... Hello All, I would like to adjust my RNAseq dataset for GC content. I used EDASeq to calculate the offset. Code data <-newSeqExpressionSet(counts=as.matrix(d$counts),featureData=feature,phenoData=data.frame(pheno),row.names=rownames(d)) dataOffset <- withinLaneNormalization(data,"gc", whi ...
edger edaseq offset written 18 months ago by alakatos100 • updated 18 months ago by Aaron Lun24k
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Tools for classifying reads from xenograft samples?
... Hello All,  I must separate human and mouse RNAs obtained by RNAseq from a tissue after xenotransplantation (human NSCs to mouse model).  Would you please suggest Bioconductor or other tools for classifying reads from xenograft samples? What is the recommended read depth and length for this kind o ...
rnaseq xenograph written 24 months ago by alakatos100
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Comment: C: Filtering DGEList object in edgeR
... Thank you. A   ...
written 2.0 years ago by alakatos100
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Comment: C: Filtering DGEList object in edgeR
... It worked. Thanks. ...
written 2.0 years ago by alakatos100
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Filtering DGEList object in edgeR
... Hello All,  I made a DGEList object. d <- DGEList(counts = COUNTS[,8:43], group = condition,genes=COUNTS$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 2.0 years ago by alakatos100 • updated 2.0 years ago by Gordon Smyth37k
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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 2.1 years ago by alakatos100
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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 2.1 years ago by alakatos100 • updated 2.1 years ago by Ryan C. Thompson7.3k

Latest awards to alakatos

Popular Question 2.1 years ago, created a question with more than 1,000 views. For barplot with ggplot2 for gene expression
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 2.1 years ago, created a question with more than 1,000 views. For limma, reference group, covariate
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Mouse Transcriptome Assay 1.0 processing and annotation
Popular Question 2.1 years ago, created a question with more than 1,000 views. For filtering out probes with no gene symbol from expressionSet
Popular Question 2.1 years ago, created a question with more than 1,000 views. For A good alternative for RDavidWebService ??
Popular Question 2.1 years ago, created a question with more than 1,000 views. For gene expression visualization: lineplot with ggplot2
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays

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