User: mh.manoj

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mh.manoj0
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Posts by mh.manoj

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Comment: C: WGCNA multiple samples
... Thanks for your answer Lluís R. Indeed my objective is to find co-expressed modules between all the 72 conditions. I think I am on the right track - using all 144 samples together and then looking at patterns of coexpressed modules. I could see clear banded patterns when I look at modules with r > ...
written 10 months ago by mh.manoj0
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WGCNA multiple samples
... Hello, From WGCNA documentation, I understand that a minimum of ~20 samples is required for robust WGCNA. I'm working with a set of 144 samples. These are two replicates for 72 different conditions. I wanted to make sure that using WGCNA in this case would be ok to identify coexpressed modules.  T ...
wgcna written 11 months ago by mh.manoj0 • updated 11 months ago by Lluís R300
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Comment: C: WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
... Thanks for your comment Peter.  I am not an expert in statistics, but from reading the article, especially section 3.2, I understand that the bicor would switch to hybrid Pearson-robust correlation if columns have MAD=NA. I guess that is what is happening in this case. I hope this is a normal behav ...
written 2.2 years ago by mh.manoj0
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Answer: A: WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
... Hi Peter, I had a problem similar to this discussion while trying to use the bicor function. I followed your instruction to use the corOptions as a literal string, but then the bicor was not implemented. Please see various combinations I tried. Could you please suggest the right usage?    > a ...
written 2.2 years ago by mh.manoj0
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Comment: C: edgeR Multifactor Design - Baseline
... I agree. The design formula should have an intercept term. When I do a classic exact test, just pairwise comparison I do get DE genes (Drug vs Placebo) at each time point. Probably, when taken as a whole (across development), there is no significantly DE genes. Thanks very much Gordon and Aaron fo ...
written 2.6 years ago by mh.manoj0
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Comment: C: edgeR Multifactor Design - Baseline
... Hi Gordon, Thanks very much for your input. I tried the two options you gave. It makes sense to reverse the factors in order to model the effect of drug effects at each time, accounting for the changes during normal development, derived from the Placebo samples. I'm a bit confused about the use of ...
written 2.6 years ago by mh.manoj0
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Comment: C: edgeR Multifactor Design - Baseline
... Thanks Aaron for your inputs. I agree, when you take out the phrase "whole developmental change", it doesn't make sense. As explained in my original post: "my objective is to identify the genes that change due to drug treatment at 2w, across development. There are normal, expected changes that hap ...
written 2.7 years ago by mh.manoj0
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Comment: C: edgeR Multifactor Design - Baseline
... Thanks Aaron. Part 1: I'm not really trying to get the effect of placebo -- I want to use this (placebo) to account for changes during development, and get the effect of treatment. Part 2: I understand that the problem is because only one of the Placebo time points is getting considered (10w or 2w ...
written 2.7 years ago by mh.manoj0
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Comment: C: edgeR Multifactor Design - Baseline
... Thanks for your comment Aaron. Below is the design matrix that was generated: > design (Intercept) TreatDrug TreatPlaceb:Time2w TreatDrug:Time2w TreatPlaceb:Time3w TreatDrug:Time3w TreatPlaceb:Time4w TreatDrug:Time4w TreatPlaceb:Time6w TreatDrug:Time6w 2S1 1 0 ...
written 2.7 years ago by mh.manoj0
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edgeR Multifactor Design - Baseline
... Hello, In my experiment, we have mice treated with drug and saline at 2 week stage. We have transcriptome data for both these treatments across five development time points - 2w, 3w, 4w, 6w and 10w. My objective is to detect the effect of drug at each time point, where the Sal accounts for changes ...
edger multiple factor design written 2.7 years ago by mh.manoj0 • updated 2.7 years ago by Gordon Smyth32k

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