User: alakatos

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alakatos80
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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$counts, old.fitted, new.fitted, dispersion=0.05) Error in raw.mat[i, , drop = FALSE] : (subscript) logical subscript too long I am not sure what I was doin w ...
written 4 weeks ago by alakatos80
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Comment: C: edgeR:fitted and partial expression values
... "Are you saying you want to regress out particular covariates and use the corrected observations for downstream analyses?" Yes. Thanks Aaron very much. It is very helpful. ...
written 4 weeks ago by alakatos80
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edgeR:fitted and partial expression values
... Hello Everyone, I have a very noise RNAseq dataset with several covariates analyzed in edgeR. design <- model.matrix(~0 + conditions + cov1 + cov2, data=pheno) d <- calcNormFactors(d, method ="TMM") d <- estimateDisp(d, design, robust=TRUE ) fit <- glmFit(d, design, dispersion=d$trend ...
edger cpm explained variance fitted model written 4 weeks ago by alakatos80 • updated 4 weeks ago by Gordon Smyth32k
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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$counts),featureData=feature,phenoData=data.frame(pheno),row.names=rownames(d)) dataOffset <- withinLaneNormalization(data,"gc", whi ...
edger edaseq offset written 5 weeks ago by alakatos80 • updated 5 weeks ago by Aaron Lun18k
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Tools for classifying reads from xenograft samples?
... Hello All,  I must separate human and mouse RNAs obtained by RNAseq from a tissue after xenotransplantation (human NSCs to mouse model).  Would you please suggest Bioconductor or other tools for classifying reads from xenograft samples? What is the recommended read depth and length for this kind o ...
rnaseq xenograph written 6 months ago by alakatos80
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Comment: C: Filtering DGEList object in edgeR
... Thank you. A   ...
written 7 months ago by alakatos80
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Comment: C: Filtering DGEList object in edgeR
... It worked. Thanks. ...
written 7 months ago by alakatos80
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Filtering DGEList object in edgeR
... Hello All,  I made a DGEList object. d <- DGEList(counts = COUNTS[,8:43], group = condition,genes=COUNTS$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 7 months ago by alakatos80 • updated 7 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 8 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 8 months ago by alakatos80 • updated 8 months ago by Ryan C. Thompson6.3k

Latest awards to alakatos

Popular Question 10 months ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 22 months ago, created a question with more than 1,000 views. For Annotating limma Results with Gene Names for Affy Microarrays
Popular Question 22 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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