User: Federico Gaiti

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Posts by Federico Gaiti

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Comment: C: Low number of replicates DESeq
... Thanks a lot. I spent a couple of days trying to figure how to make this. As usual quick reply and efficient! Best, Federico ________________________________________ From: mailinglist.honeypot@gmail.com [mailinglist.honeypot@gmail.com] on behalf of Steve Lianoglou [lianoglou.steve@gene.com] Sent: ...
written 3.7 years ago by Federico Gaiti130
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Comment: C: Low number of replicates DESeq
... Hi Mike, I am trying to make a heatmap with only a subset of differentially expressed genes. The previous email shows how I performed the DGE analsis. I used: select<-order(res$padj)[1:50] heatmap.2(assay(rld)[select,],col=rev(heat.colors(25)),trace="none") My 'res' result looks like this: ...
written 3.7 years ago by Federico Gaiti130
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Comment: C: Low number of replicates DESeq
... Thanks guys fo all the help ________________________________ From: Michael Love [michaelisaiahlove@gmail.com] Sent: Monday, 3 March 2014 10:51 PM To: Federico Gaiti Cc: Steve Lianoglou; bioconductor@r-project.org Subject: Re: [BioC] Low number of replicates DESeq hi Federico, This is correct. M ...
written 3.7 years ago by Federico Gaiti130
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Low number of replicates DESeq
... Hi Mike, I did the DGE with the mmultifactorial design combining stranded and unstranded data. Here it is: Multifactorial (considering both stranded and unstranded data) > head(CountTable) ADULT ADULT1 ADULT2 ADULT3 JUV JUV1 JUV2 JUV3 COMP COMP1 COMP2 COMP3 PRECOMP PRECOMP1 PRECOM ...
transcription go deseq2 written 3.7 years ago by Federico Gaiti130 • updated 3.7 years ago by Michael Love15k
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Comment: C: Low number of replicates DESeq
... Hi Mike, It's nice to hear this from you!I feel I'm not too far to get the DGE done So back to DGE as per my previouos email, I carefully read the DESeq2 vignette (February 19, 2014) and then did the DGE using two different models as previously suggested. Multifactorial (considering both stranded ...
written 3.7 years ago by Federico Gaiti130
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Comment: C: Low number of replicates DESeq
... No worries at all. It's all a good exercise for me. I'm learning a lot just from this email exchange. Back to the DGE and considering the situation, what would you raccomend for the DGE on DESeq2? Thanks again Federico ________________________________ From: Michael Love [michaelisaiahlove@gmail ...
written 3.7 years ago by Federico Gaiti130
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Comment: C: Low number of replicates DESeq
... Hi Mike, Thanks for reply. I see what you mean but I'm a bit confused about ht- seq count now. Please see also an open thread with Simon Anders where I'm discussing this in details: http://seqanswers.com/forums/showthread.php?p=133959& posted=1#post133959 Sorry for the crosspost I know, I just ...
written 3.7 years ago by Federico Gaiti130
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Comment: C: Low number of replicates DESeq
... Hi Steve, I carefully read the DESeq2 vignette (February 19, 2014) and then did the DGE using two different models as you suggested and then performed different contrasts. Multifactorial > head(CountTable) ADULT ADULT1 ADULT2 ADULT3 JUV JUV1 JUV2 JUV3 COMP COMP1 COMP2 COMP3 PRECOM ...
written 3.7 years ago by Federico Gaiti130
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Comment: C: Low number of replicates DESeq
... Hi Steve, thanks for the reply and sorry for all the code. I'm still a beginner in this field so I'm still learning how to correctly formulate my questions/emails. I agree with you about the PCA plot analysis. Could you just explain better to me what you mean with " If this is the case, then encod ...
written 3.7 years ago by Federico Gaiti130
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Comment: C: Low number of replicates DESeq
... Hi MiKe, thanks for useful suggestion. As you and Steve suggested, I followed the multifactorial design section in both DESeq and DESeq2 vignette and then checked the quality by sample clustering and visualization. In DESeq 1.14: CountTable=read.table("DGE.txt",header=TRUE,row.names=1) head(Coun ...
written 3.7 years ago by Federico Gaiti130

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