User: Tanvir Ahamed

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240
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Sweden
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Posts by Tanvir Ahamed

<prev • 74 results • page 1 of 8 • next >
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Convert "minfi::RGChannelSet" class from OLD to NEW
... Hi, "RGChannelSet" is a class of data in minfi package. Very recently "SummarizedExperiment" package has change their class definition and so "RGChannelSet" has changed as "RGChannelSet" class is dependent on "SummarizedExperiment". Now I have saved a data in "RGChannelSet" class and I have los ...
rgchannelset minfi summarizedexperiment written 16 days ago by Tanvir Ahamed 240
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Read .eds formated file form QuantStudio 12K Flex Software in R
... I want to read data in R form QuantStudio™ 12K Flex Software which is .eds format. Can any one please suggest any package/code for this ? ...
R bioconductor quantstudio .eds written 15 months ago by Tanvir Ahamed 240
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Answer: A: Compare control probe in 450k and EPIC
... I have found [ENmix][1] package in bioconductor is very helpful regarding this issue. Helpful readings: [Innium® HD Assay Methylation Protocol Guide][2] [1]: https://www.bioconductor.org/packages/release/bioc/html/ENmix.html [2]: http://support.illumina.com/content/dam/illumina-support/docu ...
written 18 months ago by Tanvir Ahamed 240
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(Closed) Compare control probe in 450k and EPIC
... Based on similar sample, how to compare the control probe in 450k ad EPIC ? Any help will be appreciated . ...
450k epic written 18 months ago by Tanvir Ahamed 240 • updated 18 months ago by Charles Warden4.9k
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Comment: C: Compare 450k with EPIC
... Thanks for your suggestion . Can you please tell me, it it possible to get the same result (equivalent value) for intensity on common probe for 450k and EPIC. So for that, can i compare raw data or any further normalization or other procedure if required ? ...
written 18 months ago by Tanvir Ahamed 240
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Compare 450k with EPIC
... I have the idat file form a same sample in 450k and EPIC. What is the best way to compare those results? Can i compare raw data or should I apply any specific normalization before comparison? ...
450k methylation 850k epic written 18 months ago by Tanvir Ahamed 240 • updated 7 months ago by joshmoss110
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Comment: C: Map ensembl gene id form hg38 in hg19
... Thanks your your time and reply. I have also tried with GTF files from Ensembl FTP for both GRCh37, GRCh38 and tried to map ENSG ID from GRCh38 in GRCh37 for miRNA (BioType). But could not figured out an active solution. :( ...
written 19 months ago by Tanvir Ahamed 240
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Comment: C: Map ensembl gene id form hg38 in hg19
... Example added to main question !! ...
written 19 months ago by Tanvir Ahamed 240
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Map ensembl gene id form hg38 in hg19
... I want to map all ensembl gene id form hg38 in hg19. Any help will be appreciated ? Thanks !! # Example : Loading library library(biomaRt) List of miRNA form hg38 grch38 <- useMart("ensembl",dataset="hsapiens_gene_ensembl") miRNA38 <- getBM( attributes=c("ensembl_gen ...
sequencing hg38 hg19 written 19 months ago by Tanvir Ahamed 240
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Comment: C: Updated database for miRNA
... I have used to following code to read the GTF file in R library(refGenome) pp<-ensemblGenome("C:\\Users\\Downloads") read.gtf(pp, "Homo_sapiens.GRCh38.84.chr.gtf") mm<-getGtf(pp) # Frequency table for biotype 'miRNA' table(mm$transcript_biotype) But i got number of ...
written 19 months ago by Tanvir Ahamed 240

Latest awards to Tanvir Ahamed

Popular Question 11 days ago, created a question with more than 1,000 views. For Map ensembl gene id form hg38 in hg19
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Missing value imputation for beta values of Methylation data
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Relation between "MAPINFO" and "UCSC_CpG_Islands_Name" in Illumina manifest file
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Frequency of a unique sequence in a fasta file
Popular Question 7 months ago, created a question with more than 1,000 views. For Interpretation of Beta values : Methylation data
Popular Question 8 months ago, created a question with more than 1,000 views. For Interpretation of Beta values : Methylation data
Popular Question 8 months ago, created a question with more than 1,000 views. For Relation between "MAPINFO" and "UCSC_CpG_Islands_Name" in Illumina manifest file
Popular Question 10 months ago, created a question with more than 1,000 views. For Compare 450k with EPIC
Popular Question 10 months ago, created a question with more than 1,000 views. For Interpretation of Beta values : Methylation data
Great Question 11 months ago, created a question with more than 5,000 views. For Extract sequence with header from a fasta file with specific ID given in another file
Appreciated 14 months ago, created a post with more than 5 votes. For A: How can I BLAST 4,54,871 sequences?
Supporter 22 months ago, voted at least 25 times.
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Frequency of a unique sequence in a fasta file
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Extract sequence with header from a fasta file with specific ID given in another file
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Extract sequence with header from a fasta file with specific ID given in another file
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Frequency of a unique sequence in a fasta file
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Frequency of a unique sequence in a fasta file
Scholar 2.9 years ago, created an answer that has been accepted. For A: Extract sequence with header from a fasta file with specific ID given in another
Scholar 2.9 years ago, created an answer that has been accepted. For A: Extract sequence with header from a fasta file with specific ID given in another

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