User: ghk

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ghk0
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Posts by ghk

<prev • 103 results • page 1 of 11 • next >
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
... Yes I posted a new question (https://support.bioconductor.org/p/99318/) ...
written 1 day ago by ghk0
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Filtering step in Differential analysis with RSEM values
... Dear Aaron, In this post (C: Possible ways of performing differential gene expression and analysis of RNA-Seq) Gordon gave a code for Differential analysis with RSEM values. In that he used a filtering step keeping genes that have about 10 counts or more in atleast 14 samples. Which means there are ...
edger differential gene expression rsem written 1 day ago by ghk0 • updated 1 day ago by Gordon Smyth31k
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Comment: C: Question about decideTests function and adj.p.value in "limma" R Package
... Dear Aaron, In this post (https://support.bioconductor.org/p/91054/#99294) Gordon gave a code for Differential analysis with RSEM values. In that he used a filtering step keeping genes that have about 10 counts or more in atleast 14 samples. Which means there are 14 samples in the smallest "experim ...
written 1 day ago by ghk0
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... For my data It looks like following: table(targets$Sample.type) MB1   MB2  286     80  So, on what sample number should I filter now?  Do I need to filter like this?  keep <- rowSums(y > log2(11)) >= 80 ...
written 2 days ago by ghk0
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Comment: C: Possible ways of performing differential gene expression and analysis of RNA-Seq
... Dear Gordon, In the above code I have a small doubt. In the filtering step Why you are keeping genes that have about 10 counts or more in atleast 14 samples ? why not more than 14 samples and why not only 3 samples? Could you please tell me this. Thank you ...
written 2 days ago by ghk0
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Comment: C: Calculating rpkm from counts data?
... As you said I took the total exonic length into consideration and did the further analysis. myDGEList <- DGEList(counts= expressionMatrix , genes= geneDataFrame) Here geneDataFrame is having a column length corresponding to each row in the expression matrix. To calculate RPKM values I did like ...
written 2 days ago by ghk0
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Comment: C: Calculating rpkm from counts data?
... Ok. I dont have any problem with this now. I have transformed the counts data into rpkmMatrix as you said. I want to make a density plot with the rpkm values of the samples. How can I do this? ...
written 3 days ago by ghk0
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Comment: C: Calculating rpkm from counts data?
... If not this, can I take the gene which has highest transcript_length from the above mentioned multiple IDs? I mean  ENSG00000083642  PDS5B  7497 ...
written 5 days ago by ghk0
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Comment: C: Calculating rpkm from counts data?
... Ensembl Gene ID     Symbol   transcript_length ENSG00000083642  PDS5B  797 ENSG00000083642  PDS5B  906 ENSG00000083642  PDS5B  684 ENSG00000083642  PDS5B  1889 ENSG00000083642  PDS5B  972 ENSG00000083642  PDS5B  5246 ENSG00000083642  PDS5B  4238 ENSG00000083642  PDS5B  581 ENSG00000083642   ...
written 6 days ago by ghk0
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Comment: C: Calculating rpkm from counts data?
... I got the transcript length for Ensembl Ids. But Each ensembl ids having multiple transcript lengths. Which one should I use? ...
written 6 days ago by ghk0

Latest awards to ghk

Popular Question 6 months ago, created a question with more than 1,000 views. For Heatmap with error message: `x' must be a numeric matrix
Popular Question 15 months ago, created a question with more than 1,000 views. For Heatmap with error message: `x' must be a numeric matrix
Rising Star 16 months ago, created 50 posts within first three months of joining.

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