User: alakatos

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alakatos110
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United States
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3 weeks, 3 days ago
Joined:
4 years, 11 months ago
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a*******@uci.edu

Posts by alakatos

<prev • 75 results • page 1 of 8 • next >
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Comment: C: Finding gene targets for a list of transcription factors
... Thank you all for your help and advice. Anita ...
written 24 days ago by alakatos110
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Finding gene targets for a list of transcription factors
... Hello All, I am reaching out for your advice. Would you please recommend tools preferably in Bioconductor for the following problem: I have a list of transcription factors. At first, I must find all the possible downstream gene targets, then retrieve all the possible interactions (edges) between ...
transcription factors regulatory gene network gene targets written 29 days ago by alakatos110 • updated 26 days ago by svlachavas740
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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$counts, old.fitted, new.fitted, dispersion=0.05) Error in raw.mat[i, , drop = FALSE] : (subscript) logical subscript too long I am not sure what I was doin w ...
written 21 months ago by alakatos110
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Comment: C: edgeR:fitted and partial expression values
... "Are you saying you want to regress out particular covariates and use the corrected observations for downstream analyses?" Yes. Thanks Aaron very much. It is very helpful. ...
written 21 months ago by alakatos110
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edgeR:fitted and partial expression values
... Hello Everyone, I have a very noise RNAseq dataset with several covariates analyzed in edgeR. design <- model.matrix(~0 + conditions + cov1 + cov2, data=pheno) d <- calcNormFactors(d, method ="TMM") d <- estimateDisp(d, design, robust=TRUE ) fit <- glmFit(d, design, dispersion=d$trend ...
edger cpm explained variance fitted model written 21 months ago by alakatos110 • updated 21 months ago by Gordon Smyth38k
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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$counts),featureData=feature,phenoData=data.frame(pheno),row.names=rownames(d)) dataOffset <- withinLaneNormalization(data,"gc", whi ...
edger edaseq offset written 21 months ago by alakatos110 • updated 21 months ago by Aaron Lun25k
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Tools for classifying reads from xenograft samples?
... Hello All,  I must separate human and mouse RNAs obtained by RNAseq from a tissue after xenotransplantation (human NSCs to mouse model).  Would you please suggest Bioconductor or other tools for classifying reads from xenograft samples? What is the recommended read depth and length for this kind o ...
rnaseq xenograph written 2.2 years ago by alakatos110
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Comment: C: Filtering DGEList object in edgeR
... Thank you. A   ...
written 2.3 years ago by alakatos110
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Comment: C: Filtering DGEList object in edgeR
... It worked. Thanks. ...
written 2.3 years ago by alakatos110
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Filtering DGEList object in edgeR
... Hello All,  I made a DGEList object. d <- DGEList(counts = COUNTS[,8:43], group = condition,genes=COUNTS$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 2.3 years ago by alakatos110 • updated 2.3 years ago by Gordon Smyth38k

Latest awards to alakatos

Popular Question 2.3 years ago, created a question with more than 1,000 views. For barplot with ggplot2 for gene expression
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 2.3 years ago, created a question with more than 1,000 views. For limma, reference group, covariate
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Mouse Transcriptome Assay 1.0 processing and annotation
Popular Question 2.3 years ago, created a question with more than 1,000 views. For filtering out probes with no gene symbol from expressionSet
Popular Question 2.3 years ago, created a question with more than 1,000 views. For A good alternative for RDavidWebService ??
Popular Question 2.3 years ago, created a question with more than 1,000 views. For gene expression visualization: lineplot with ggplot2
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 3.5 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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