User: Jo

gravatar for Jo
Jo10
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10
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Last seen:
3 years, 5 months ago
Joined:
3 years, 10 months ago
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t******@gmail.com

Posts by Jo

<prev • 14 results • page 1 of 2 • next >
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UPC RNA-Seq individual samples
... Hello, I am trying to do a UPC normalization on a GEO dataset. Is there a way to produce read count files such that I can do the UPC normalization on all samples at once rather than each sample individually? I want to have one output file for the dataset. Is this possible? Please let me know. ...
rnaseq scan.upc upc written 3.5 years ago by Jo10 • updated 3.5 years ago by Stephen Piccolo560
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RSubread 0% mapping
... Hi, I am trying to produce ReadCount values for a RNA-Seq dataset using the Rsubread package. I first converted each SRA file from the GEO site for the dataset to a fastq file. I then concatenated all of the fastq files into one file. Then I gzipped the file. I then used the rsubread package to p ...
rsubread featurecounts mapping align written 3.5 years ago by Jo10
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RNA-Seq Read Counts for SCAN.UPC
... Hello, I am trying to generate RNA-Seq read counts for an RNA-Seq dataset from the NCBI site. I am then going to use the read count files to run a UPC normalization on the dataset using SCAN.UPC.  How can I obtain RNA-Seq read count files using R? Please advise.   ...
rnaseq scan.upc written 3.5 years ago by Jo10 • updated 3.5 years ago by Stephen Piccolo560
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Comment: C: Comparing SCAN Q.value with Meta-Analyses Q.Value
...   Hello, I checked the value and it was in the Q-Value Column. Here is the code I used to generate the the Q-values for the meta-analysis: library(meta) a <- eset1146[,2] b <- eset22610[,2] c <- eset58538[,2] d <- eset43995[,2] intersectgenes <- Reduce(intersect, list(a,b,c,d)) ...
written 3.6 years ago by Jo10
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Comment: C: Joint Preprocessing of RNA-Seq and Microarray datasets
... Thanks for the reply. Is it possible to do a meta-analyses combining RNA-Seq datasets and Microarray datasets? If so how? Thanks in advance. ...
written 3.6 years ago by Jo10
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Comment: C: Joint Preprocessing of RNA-Seq and Microarray datasets
... I want to normalize, remove batch effects (ComBat), and run limma on the datasets jointly. ...
written 3.6 years ago by Jo10
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Joint Preprocessing of RNA-Seq and Microarray datasets
... Hi, I would like to jointly pre-process RNA-Seq datasets and Microarray datasets together. Are there any pipelines or ways to do this? Please advise. Thanks   ...
rnaseq microarray preprocessing written 3.6 years ago by Jo10 • updated 3.6 years ago by Gordon Smyth37k
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Comparing SCAN Q.value with Meta-Analyses Q.Value
... Hi,   I am trying to compare the q.values produced by a dataset from a normalization done by SCAN against the q.values from the same dataset but from a meta-analyses. I want the comparison to be in the form of a scatter plot. I want this plot to show that there is a correlation between the q.value ...
scan.upc meta scan q value written 3.6 years ago by Jo10
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Comment: C: Choosing most accurate gene symbol from multiple gene symbols
... Awesome thanks.  ...
written 3.8 years ago by Jo10
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Choosing most accurate gene symbol from multiple gene symbols
... Hi, I am trying to map Transcript ID's of the HuGene-1_0-st-v1 affy chip to their corresponding Gene Symbols. When I do this I am often getting multiple gene symbols for Transcript ID's.  ex:  8029669 --> CT47A1 /// CT47A6 /// CT47A11 /// CT47A7 /// CT47A2 /// CT47A8 /// CT47A9 /// CT47A3 /// C ...
gene symbol transcript_id written 3.8 years ago by Jo10 • updated 3.8 years ago by James W. MacDonald50k

Latest awards to Jo

Popular Question 3.4 years ago, created a question with more than 1,000 views. For Oligo package RMA() function giving error

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