User: manasishah86

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manasishah8630
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Posts by manasishah86

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Comment: C: paired analysis using metagenomeSeq
... Thanks Joe, what alternative would you suggest for in the meanwhile? An option that outputs standard error. The topTable function in limma+voom though extremely fast, do not provide standard errors -Manasi ...
written 2.6 years ago by manasishah8630
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paired analysis using metagenomeSeq
... Can we use the fitFeatureModel function in metagenomeSeq to determine log fold changes adjusting for paired samples i.e for example tumor and  tumor adjacent biopsy microbiome samples? i.e in the tutorial can we add a pair factor that denotes samples from the same host as P1, P2 and so on in the mod ...
metagenomeseq logfc standard error paired samples written 2.6 years ago by manasishah8630 • updated 2.6 years ago by mariamake00110
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Comment: C: Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth,
... I have tried to keep my R session clean with more discipline (and developed more faith on the reproducibility of my code and results) since this post :) since this post. Thank you  ...
written 2.7 years ago by manasishah8630
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Comment: C: Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth,
... Thank you for your response. I had some features with very low variance. I removed these and did not see this error anymore. Is there any variance threshold one should keep in mind when using edgeR / limma?   ...
written 2.7 years ago by manasishah8630
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Comment: C: Confidence intervals on edgeR logFC
... Thank you so much for this answer! I am building a random effects model to compare log fold change across several studies. I had used DESEq2 initially since they provide a log fold change SE and have been previously documented to be used with microbiome data (which is what I am working with).  Howe ...
written 2.7 years ago by manasishah8630
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Comment: C: No residual df, setting dispersion to NA, Error: 'qr' and ''y' must have same nu
... Same error Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth,  :    newsplit: out of vertex space if I use descriptive names at each step: x_dge, x_norm, x > dim(x_norm) [1] 1168   10 > dim(design) [1] 10  6 > dim(x_dge) [1] 1168   10 > dim(gene_table) [1] ...
written 2.8 years ago by manasishah8630
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Comment: C: No residual df, setting dispersion to NA, Error: 'qr' and ''y' must have same nu
... Even further edit, I seemed to have fixed the coerce error, I took the exact same code for a similar study that worked and used it for another subset Got a new error and this seems to be the final one: Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth,  :    newsplit: ...
written 2.8 years ago by manasishah8630
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Comment: C: No residual df, setting dispersion to NA, Error: 'qr' and ''y' must have same nu
... Further edit: I cleared my environment and realized there were some old objects it was calling. Now I get a new error Error in as.vector(x, mode) :    cannot coerce type 'closure' to vector of type 'any' in the estimateDisp(x, design) step how did my x become of type closure? ...
written 2.8 years ago by manasishah8630
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Comment: C: No residual df, setting dispersion to NA, Error: 'qr' and ''y' must have same nu
... Hi James, I checked my dimensions and have edited the question. I did try posting the entire code multiple times earlier but it kept giving me some formatting error when I tried to submit possibly because I copied it directly from my R console.  My design matrix has 6 columns counting the intercept ...
written 2.8 years ago by manasishah8630
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Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : newsplit: out of vertex space in paired edgeR comparison
... I am getting  a warning for estimateDisp : "In estimateDisp(x, Design) : No residual df: setting dispersion to NA" Then followed by an error in glmFit(x, Design) : Error in qr.coef(qr(design), matrix(beta.mean, nrow= nlibs, ncol = ngenes 'qr' and 'y' must have same number of genes Phenotype < ...
edger model.matrix paired samples estimatedisp written 2.8 years ago by manasishah8630 • updated 2.8 years ago by Gordon Smyth37k

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