User: J. Smith

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J. Smith50
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Posts by J. Smith

<prev • 38 results • page 1 of 4 • next >
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Comment: C: What are good packages to find Differentially Expressed Genes from RNASeq RSEM a
... Dear Dr. Blighe, Greetings of the Day!!! I once again read the description of the RNAseq - IlluminaHiSeq_RNASeqV2 [LUAD dataset][1] from the UCSC Xena. [Description][2]: The gene expression profile was measured experimentally using the Illumina HiSeq 2000 RNA Sequencing platform by the Universi ...
written 4 months ago by J. Smith50
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Comment: C: What are good packages to find Differentially Expressed Genes from RNASeq RSEM a
... OK. Many many thanks Dr. Blighe. ...
written 4 months ago by J. Smith50
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Comment: C: What are good packages to find Differentially Expressed Genes from RNASeq RSEM a
... Thank you again Dr. Blighe. I found that among those 56493 Ensembl genes 19708 are protein-coding genes and 6513 ncRNA genes, 14086 lncRNA genes, 10074 processed_pseudogenes and 2464 unprocessed_pseudogenes. So, may I safely remove those 6513 ncRNA genes, 14086 lncRNA genes, 10074 processed_pseudoge ...
written 4 months ago by J. Smith50
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Comment: C: What are good packages to find Differentially Expressed Genes from RNASeq RSEM a
... Dear Dr. Blighe, I have obtained TCGA RNASeq raw counts data through TCGAbiolinks for some cancers. In all cancers there are same number of ensemble genes (~56000) for which counts values are available. After following your code using AnnotationDbi, only ~26000 ensemble genes have matching official ...
written 4 months ago by J. Smith50
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Comment: C: What are good packages to find Differentially Expressed Genes from RNASeq RSEM a
... OK. Thanks a lot Dr. Blighe... ...
written 4 months ago by J. Smith50
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Comment: C: What are good packages to find Differentially Expressed Genes from RNASeq RSEM a
... Many many thanks Dr. Blighe... Another question I want to ask, suppose corresponding to multiple ensemble gene ids, I get one official gene symbol. Then how should I calculate gene expression/ counts of that official gene symbol from the gene expressions /counts of multiple ensemble genes? And simil ...
written 4 months ago by J. Smith50
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Comment: C: What are good packages to find Differentially Expressed Genes from RNASeq RSEM a
... Hello Dr. Blighe. Actually I can download TCGA RNASeq data directly from the TCGA portal. But the problem is when I am downloading data using TCGABiolinks, I am getting ~56000 ensemble genes and their corresponding gene expressions. But I want to get gene expressions data with official gene symbols ...
written 4 months ago by J. Smith50
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Comment: C: What are good packages to find Differentially Expressed Genes from RNASeq RSEM a
... Ok. Thanks a lot. I got it... ...
written 4 months ago by J. Smith50
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Comment: C: What are good packages to find Differentially Expressed Genes from RNASeq RSEM a
... Thanks so much Kevin. ...
written 4 months ago by J. Smith50
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Comment: C: How to analyze TCGA data downloaded by TCGA2STAT using TCGAbiolinks package
... Thanks so much Kevin. ...
written 4 months ago by J. Smith50

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Popular Question 24 months ago, created a question with more than 1,000 views. For Normalisation before log2 transformation or after in Microarray Gene expression data?

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