User: mheydarpour

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mheydarpour10
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1 year, 11 months ago
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m**********@bwh.harvard.edu

Posts by mheydarpour

<prev • 46 results • page 1 of 5 • next >
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Comment: C: Remove batch effect using individuals as random in the model in Limma
... Hi Aaron, I run my data using "duplicateCorrelation" and considered batch as block in the model. But I don't know why I got very large "LogFC" for many genes in my output. My data is normalized using Quantile normalization and I have no "NA" in my gene-expression file. Any comment? Gene-ID        ...
written 11 days ago by mheydarpour10
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Comment: C: Remove batch effect using individuals as random in the model in Limma
... Thanks Aaron for the info and the codes. But, my problem is batch situation. All my Cases=37 are in the Batch 7, and the rest of patients are separated in Batch from 1 to 7. It means I have no Cases in batch 1 to 6. That's why I decided treat patients as a random effect in the model. But I don't kn ...
written 12 days ago by mheydarpour10
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Remove batch effect using individuals as random in the model in Limma
... I have 130 individuals with their RNAseq data in 7 batches treated in a Case-Control study (Case=37 and Control=93). I would like to run differential gene expression analysis for 18258 genes for this study in Limma. When I read some discussions about removing batch effect in the model through Biocon ...
block batch effect limma design matrix random effects coeficents non estimable written 12 days ago by mheydarpour10 • updated 12 days ago by Aaron Lun17k
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Comment: C: handling missing data (NA) for methylaion analysis in Limma
... CpG2 matrix : first column of this matrix is "CpG-sites-Name" and first row is "Sample-Id-Name". ...
written 29 days ago by mheydarpour10
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Comment: C: handling missing data (NA) for methylaion analysis in Limma
... typeof(CpG2) gave me "character" ...
written 29 days ago by mheydarpour10
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Comment: C: handling missing data (NA) for methylaion analysis in Limma
... I tried this: CpG2 <- as.matrix(CpG) run: fit <- lmFit(CpG2, design) Error: Error in rowMeans(y$exprs, na.rm = TRUE) : 'x' must be numeric ...
written 29 days ago by mheydarpour10
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Comment: C: handling missing data (NA) for methylaion analysis in Limma
... No, when I run "typeof(CpG)", it gave me "list" ...
written 29 days ago by mheydarpour10
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Comment: C: handling missing data (NA) for methylaion analysis in Limma
... Thanks Aaron for you explanation. My CpG-data matrix is numeric with some "NA" , however, I still got the same error when I run Limma with this design matrix: design=model.matrix(~0+age+pheno) where age is continuous variable and pheno is categorical outcome (0,1) What would be the problem that ...
written 4 weeks ago by mheydarpour10
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Comment: C: handling missing data (NA) for methylaion analysis in Limma
... But when I run "lmFit", I got the following error in Limma: fit=lmFit(CpG, design) Error in rowMeans(y$exprs, na.rm = TRUE) : 'x' must be numeric and I also have problem for Normalization of these Beta-values   ...
written 4 weeks ago by mheydarpour10
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handling missing data (NA) for methylaion analysis in Limma
... I have a final report methylation data for ~800k rows for CpG sites for 50 samples. There are many missing-values (NA) in this dataset which I have a problem when I want use Normalization and also differential methylation analysis in Limma. I just provide you a small sample of my data as follows: (V ...
normalization limma methylation missing data written 4 weeks ago by mheydarpour10 • updated 4 weeks ago by Aaron Lun17k

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