User: sarahmanderni

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Posts by sarahmanderni

<prev • 27 results • page 1 of 3 • next >
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Microarray batch effect correction
... Hi, I intend to integrate two microarray datasets with imbalanced outcome. First of all which method has shown the most robust results in this context. My current options are ComBat and RUV-2. Second, I searched on how to use ComBat. I found [this article][1] highlighting the fact that taking int ...
microarray batch effect written 20 days ago by sarahmanderni50
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Comment: C: TMM normalization factors in RNA-seq analysis
... Do you have experience of applying it over TPM values? ...
written 26 days ago by sarahmanderni50
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Comment: C: TMM normalization factors in RNA-seq analysis
... Makes sense. Will check the paper again, thanks. ...
written 26 days ago by sarahmanderni50
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Comment: C: TMM normalization factors in RNA-seq analysis
... I have nt produced the data myself; but yes the distribution of the reads vary significantly. Can you elaborate a little more what do you mean by robust measure and in what way the distribution affects? ...
written 26 days ago by sarahmanderni50
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TMM normalization factors in RNA-seq analysis
... Hi, To my understanding, the main aim in TMM normalization is to account for library size variation between samples of interest. I have a simulated RNA-seq data with equal library sizes for all samples. I ran TMM normalization and I expected to find all normalization factors (from calcNormFactors() ...
tmm normalization rna-seq written 27 days ago by sarahmanderni50 • updated 26 days ago by h.mon8.7k
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Comment: C: mRNA expression levels association
... Thanks. I also was thinking of calculating the correlation and showing it with a scatter plot. But I am wondering does this have any biological meaning? I mean suppose I got high correlation value does this say anything to the biologists? ...
written 22 months ago by sarahmanderni50
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mRNA expression levels association
... Hi all, I was wondering what is the most efficient way of investigating the association of expression levels of two different genes in an RNA-seq experiment. I mean simply, if you want to check if gene A and gene B are associated to each other for different samples. Do you think a scatter plot coul ...
rna-seq written 22 months ago by sarahmanderni50 • updated 22 months ago by TriS3.0k
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Comment: C: TopHat with older versions of Bowtie
... Actually it still produces the same error. Is it very different if I use the combination of bowtie2 and tophat2 instead of combination of bowtie1 and tophat2? ...
written 3.3 years ago by sarahmanderni50
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TopHat with older versions of Bowtie
... Hi,   I wanted to ask if it is possible to run TopHat 2 with Bowtie 1. I need to mimic an already done experiment with this trend. But, running following code I got shown error: module add samtools module add bowtie/1.0.0 module add tophat/2.0.4 tophat -o output -p 12 -r 100 --mate-std-dev 110 -- ...
tophat bowtie written 3.3 years ago by sarahmanderni50 • updated 3.3 years ago by Devon Ryan70k
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Reference genome for mapping RNA-seq spike-in dataset
... Using spike-in controls is a common way of evaluating statistical methods while finding differentially expressed genes. Having Fastq files containing ERCC controls and the corresponding gtf file for the ERCCs, how can one does the alignment step with TopHat? For instance if the samples are from huma ...
alignment rna-seq written 3.3 years ago by sarahmanderni50 • updated 3.3 years ago by karl.stamm3.2k

Latest awards to sarahmanderni

Popular Question 20 days ago, created a question with more than 1,000 views. For TopHat with older versions of Bowtie
Supporter 26 days ago, voted at least 25 times.
Great Question 21 months ago, created a question with more than 5,000 views. For Paired-End Bam Files
Popular Question 21 months ago, created a question with more than 1,000 views. For Detection Of Alignment Algorithm Based On Bam Files
Popular Question 21 months ago, created a question with more than 1,000 views. For How To Convert Hgnc Gene Symbols To Gene Full Description?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Paired-End Bam Files
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Gene-Specific Normalization In Rna-Seq
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Reference genome for mapping RNA-seq spike-in dataset
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How To Convert Hgnc Gene Symbols To Gene Full Description?

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