User: agm

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Posts by agm

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Why does MEDIPS only import read 1 when paired=TRUE for MEDIPS.createSet()function ?
... Hello, I am wondering why the MEDIPS.createSet() uses isFirstMateRead=T and isSecondMateRead=F when paired=TRUE? For example, I have a PE bam file that contains only properly paired and mapped reads with 54,073,380 reads(~27M R1 and 27M R2). When I import with: sample <- MEDIPS.createS ...
medips #medips written 4 weeks ago by agm0
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Comment: C: model matrix for edgeR paired-design with batch effect
... what if the design was: group <- factor(c("wt","wt","wt","wt","ko","ko","ko","ko")) subject <- as.factor(c(1,2,3,4,1,2,3,4)) batch <- as.factor(c(1,1,2,2,1,1,2,2)) ie: one set of individuals sequenced day 1, different set of individuals sequenced day 2 would the design sti ...
written 3 months ago by agm0
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Comment: C: Data downloaded from GEO has raw transcript count matrix- can I still use tximpo
... Thank you! They were positive exclamations not negative ones- I completely understand the time constraint. ...
written 5 months ago by agm0
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Comment: C: Model matrix for longitudinal pairwise rna-seq data: linear regression or linear
... You are right. Sorry about that. Fixed example: `file <- 1:12` `individual<- c(rep(1,4),rep(2,4),rep(3,4))` `timepoint <- rep(1:4,3)` `status <- rep(c("uninfected","infected","infected","infected"),3)` `df <- as.data.frame(cbind(file,individual, timepoint,status))` Comparison ...
written 5 months ago by agm0
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Data downloaded from GEO has raw transcript count matrix- can I still use tximport? Collapse raw transcript count matrix to GENE LEVEL
... Hello, I have data as raw count matrix with ensembl transcript identifiers. I have successfully made a tx2gene table from a gtf file, but am stuck. I do not have individual files from Salmon or other transcript level packages which is the input for tximport. Please help!!!!!!!! ...
tximport collapse written 5 months ago by agm0 • updated 5 months ago by Michael Love26k
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Model matrix for longitudinal pairwise rna-seq data: linear regression or linear mixed model?
... Hello, I am looking for statistical expertise to figure out if I have set up my model matrix correctly. I am going to give an example info table that represents my experimental design. I have read the limma and edgeR documentation through and through and cannot find a clear example of this. DESIGN ...
limma model matrix linear regression written 5 months ago by agm0

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