User: Natasha

Natasha440
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Posts by Natasha

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... Dear List, I have an experiment with 3 WT (GBT) and 3 KO (GAT) mice, each with 4 time points: 0h,2h,8h,24h. The PI is interested in the overall effect of KO vs WT (at each time point and overall effect too). From the PCA plot I could see that time has a large effect compared to the groups. I thus ...
written 5.4 years ago by Natasha440 • updated 5.4 years ago by Remo Sanges20
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... Dear Prof. Smyth, Thank you for your response. True, I did not realise my mistake of passing a design matrix to the classic method! I guess, in trying various combinations I managed to confuse myself. It worked now! Many Thanks, Natasha -----Original Message----- From: Gordon K Smyth [mailto:s ...
written 5.4 years ago by Natasha440
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... Hi Steve, Thanks your reply. The information you asked for is below: > dim(y2.filt$counts) [1] 4514 6 > dim(design2) [1] 6 3 Many Thanks, Natasha -- -----Original Message----- From: mailinglist.honeypot@gmail.com [mailto:mailinglist.honeypot@gmail.com] On Behalf Of Steve Lianoglou Sent ... written 5.4 years ago by Natasha440 2 answers 1.1k views 2 answers ... Dear Prof. Smyth, Thank you for your reply. Yes, I eventually did upgrade and realised that the warning message was no longer there. However, if I may ask a related question. I decided to try the same data below (but as an unpaired analysis) and got an error at the commonTagwiseDisp step. (Latest ... written 5.4 years ago by Natasha440 2 answers 1.1k views 2 answers ... Dear List, Sorry for the repost realised I forgot to add some info, also attached BCV plot. I am also trying edgeR on my data (3 groups, 2 reps each). Bacterial samples. However, when I run the following code: I get a warning message and wanted to know it's significance in downstream analysis. -- ... written 5.4 years ago by Natasha440 1 answers 1.3k views 1 answers ... Dear Michael, Thank you for your quick response, I shall try what you say after upgrading R and relevant packages. Many Thanks, Natasha -- From: Michael Love [mailto:michaelisaiahlove@gmail.com] Sent: 14 May 2013 14:39 To: Natasha Sahgal Cc: bioconductor@r-project.org Subject: Re: [BioC] DESeq ... written 5.4 years ago by Natasha440 2 answers 1.1k views 2 answers ... Dear List, I am also trying edger on my data (3 groups, 2 reps each). Bacterial samples. design condition pair 1 Cont 1 2 Cont 3 3 Trt1 1 4 Trt1 3 5 Trt2 1 6 Trt2 3 However, when I run the following code: I get a warning message and w ... written 5.4 years ago by Natasha440 • updated 5.4 years ago by Gordon Smyth35k 1 answers 1.3k views 1 answers ... Sorry forgot the sessionInfo! Added at the end now -- From: Natasha Sahgal Sent: 14 May 2013 12:29 To: bioconductor@r-project.org Subject: DESeq multifactor design paired analysis Dear List, I have a dataset with 3 conditions (control and 2 treatments), 2 replicates each. Initially I carried ou ... written 5.4 years ago by Natasha440 1 answer 1.3k views 1 answer ... Dear List, I have a dataset with 3 conditions (control and 2 treatments), 2 replicates each. Initially I carried out a normal analysis in DESeq - each treatment vs the control, but later was told it needed to be a paired analysis. Thus, just to be consistent I decided to use DESeq itself. However ... written 5.4 years ago by Natasha440 0 answers 401 views 0 answers ... Dear Alejandro, Thank you for your reply, sorry for the delayed response I have been away. This is the output: > gns <- as.character(goi$Gene.ID) > all( gns %in% levels( geneIDs( ecs ) ) ) [1] FALSE > gns %in% levels( geneIDs( ecs ) ) [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TR ...
written 5.5 years ago by Natasha440

Latest awards to Natasha

Popular Question 5.4 years ago, created a question with more than 1,000 views. For Affymetrix annotation using R or NetAffx
Popular Question 5.4 years ago, created a question with more than 1,000 views. For coefficient not estimable (limma warning)

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