User: Vani

gravatar for Vani
Vani20
Reputation:
20
Status:
New User
Location:
United States
Last seen:
3 years, 9 months ago
Joined:
4 years, 4 months ago
Email:
j*********@yahoo.com

Posts by Vani

<prev • 22 results • page 2 of 3 • next >
10
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6 follow
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Standard error and effect size from Limma
... Is it possible to find the standard error and effect size of a dataset using limma's lmfit and toptable? Please advise. ...
limma toptable effect size standard error written 4.2 years ago by Vani20 • updated 4.2 years ago by Gordon Smyth38k
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Comment: C: Log2FC values very small with SCAN
... I am getting small values for the Affymetrix Human Genome U133 Plus 2.0 Array. The sample size is around 68. I am using limma's lmFit and toptable to generate the log2FC. I tried FRMA and the values ranged from -1.3 to 1.3. Here is my code: #Load data using InSilicoDb eset21610 <- getDataset(" ...
written 4.2 years ago by Vani20 • updated 4.2 years ago by Gordon Smyth38k
1
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2
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781
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Log2FC values very small with SCAN
... Hi, ​I am using the SCAN method to normalize several geo datasets. The resulting Log2FC values of the normalized eset are very small (between -.5 and .5). Is this normal? Not sure why the values are so small. Please advise.   ...
scan log2fc written 4.2 years ago by Vani20 • updated 4.2 years ago by Gordon Smyth38k
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LmFit and eBayes on merged ESET giving errors
... Hi, I am trying to run Limma's LmFit() and eBayes() on a ESET merged using InSilicoMerging. Both functions are giving me errors. The Heart_Failure column contains the values yes, no and NA.  Here is my code: eset57338 <- (getDataset("GSE57338", "GPL11532",format = "CURESET", norm = "SCAN", fe ...
limma error ebayes eset written 4.3 years ago by Vani20 • updated 4.3 years ago by James W. MacDonald51k
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Comment: C: Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimens
... Thank You! It worked ...
written 4.3 years ago by Vani20
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Comment: C: Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimens
... design1: 38 rows & eset21610: 19528 rows, 68 colnames.  There were 30 NA's, 30 yes heart failure, and 8 no heart failure in the Heart_Failure column. ...
written 4.3 years ago by Vani20
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Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension
... Hi, I am trying to run limma's lmFit on a geo dataset pertaining to heart failure. Whenever I run the lm.fit command I get the error: Lm.fit() giving Error in lm.fit(design, t(M)) : incompatible dimension. I am trying to run the differential expression on the non-failing and failing hearts. The Hea ...
limma error differential expression design matrix eset written 4.3 years ago by Vani20 • updated 4.3 years ago by Aaron Lun25k
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Limma on a merged ESET
... Is it possible to run limma on an ESET containing the data of 4 normalized datasets that have been merged? If yes please advise. I am trying to use the two functions: lmFit and eBayes on the ESET.  ...
microarray limma eset written 4.3 years ago by Vani20
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Comment: C: Creating an Expression Set with a csv file
... Cool. Thanks. ...
written 4.3 years ago by Vani20
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Comment: C: Creating an Expression Set with a csv file
... The csv file contains the annotation of the HuGene-1_0-st-v1 affymetrix chip. So basically it has all the info like enterzID, GeneSymbol etc. Would it still be considered  to be a pheno data object? ...
written 4.3 years ago by Vani20

Latest awards to Vani

Great Question 3.8 years ago, created a question with more than 5,000 views. For Creating an Expression Set with a csv file
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Standard error and effect size from Limma
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Meta-Analysis after running limma on a normalized dataset
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Creating an Expression Set with a csv file
Popular Question 3.8 years ago, created a question with more than 1,000 views. For Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension

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