User: zoppoli pietro

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10
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New User
Location:
United States
Last seen:
1 week, 3 days ago
Joined:
7 years, 2 months ago
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z*************@gmail.com

Posts by zoppoli pietro

<prev • 8 results • page 1 of 1 • next >
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Comment: C: EDASeq, RUVSeq and edgeR together
... Hi Davide, following your tips I changed this dispersion: disp <- estimateGLMCommonDisp(counts(dataOffset), design, offset=-offst(dataOffset)) with this dispersion disp2 <- estimateDisp(counts(dataOffset),design, offset=-offst(dataOffset)) and changed the fit step: fit <- glmFit(c ...
written 21 days ago by zoppoli pietro10
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EDASeq, RUVSeq and edgeR together
... Hi, I'd like to use together EDASeq,RUVSeq and edgeR I'd like to know if It's correct to run the folling code According to EDASeq manual: dataOffset <- withinLaneNormalization(data,"gc",which="upper",offset=TRUE) dataOffset <- betweenLaneNormalization(dataOffset,which="upper",offset=TRUE ...
edger edaseq ruvseq written 26 days ago by zoppoli pietro10 • updated 25 days ago by davide risso750
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Comment: C: use EDAseq normalized data as input of DESeq2
... Sorry to bother but I'd like to know if it's correct to pass the normCounts(dataOffset) obtained in the previous example directly to voom in order to to process RNA-Seq data prior to linear modelling in limma. I'm trying to make a comparison on the different pipelines to make a DEA from my RNAseq d ...
written 5 months ago by zoppoli pietro10
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Comment: C: use EDAseq normalized data as input of DESeq2
... Thanks a lot! Everything much clear now! Pietro ...
written 5 months ago by zoppoli pietro10
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Answer: A: use EDAseq normalized data as input of DESeq2
... Sorry, I was unclear in my question. I know the DESeq2 vignette but in the EDAseq I didn't find how to handle DESeq2 while there is EgdeR and DESeq. I was wondering if there was something like this (reported in EDAseq): ## ----deseq------------------------------------------------ library(DESeq) ...
written 5 months ago by zoppoli pietro10
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use EDAseq normalized data as input of DESeq2
... Hi   I'd like to use EDAseq normalized data as input of DESeq2. I found the vignette for DESeq but not for DESeq2. Is there a way to do DESeq2 DEA starting from  EDAseq normalized data ?  I understand I can use this dds <- DESeqDataSetFromMatrix(countData = cts,                             ...
edaseq deseq2 written 5 months ago by zoppoli pietro10
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Answer: A: TDARACNE:::ToTheGraph_timeShiftmax2 doesn't support more than 1000 edges
... Hi Sergi, the reason the maximum number of edges hardcoded to 1000 is that the algorithm is supposed to work with small-medium networks. 1000 edge is far above the limits I suggest to use the algorithm, I didn't want people use it so far away from it's limits. Probably I should have used a check ...
written 2.9 years ago by zoppoli pietro10
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lumi, Illumina Methylation 450k, and robust methylation calls
... Tim Rayner writes: > > Hi, > > I have recently started to use the lumi package to analyse some > Illumina Human Methylation 450k data, and I have run into some > problems which seem to revolve around division by zero in the > gammaFitEM() function. I have adjusted the colour b ...
lumi written 7.2 years ago by zoppoli pietro10 • updated 7.2 years ago by Tim Rayner270

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