User: lalchungnungabt17

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Posts by lalchungnungabt17

<prev • 9 results • page 1 of 1 • next >
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DESeq2 coldata and count data subset
... Hi, I have DESeqDataSet object 'ddsHTSeq' which contain multiple sample types. But i want to perform differential gene expression analysis only at a subset of this data. I have subset the data and ran DESeq, but the result is not what i was expected, since i knew some genes which were among the mo ...
deseq2 differential gene expresssion written 3 months ago by lalchungnungabt170 • updated 3 months ago by Martin Morgan ♦♦ 23k
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Comment: C: Reading 450k data in minfi
... Hi, Thanks for the comment! However, my problem is there is no basenames itself in the first place! ...
written 3 months ago by lalchungnungabt170
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Comment: C: Reading 450k data in minfi
... Illumina Inc. [Heading] Descriptor File Name BS0010894-AQP_content.bpm Assay Format Infinium 2 Date Manufactured 06/11/2008 Loci Count 485553 ...
written 3 months ago by lalchungnungabt170
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Reading 450k data in minfi
... Hi, I have downloaded 450k data and want to read in minfi. When i downloaded the file it comes with csv, txt and excel files, but it does not have any idat files. I have tried to read the csv file in minfi according to the tuitorial. But i get below error. Did anybody have the same problem and kno ...
minfi 450k written 3 months ago by lalchungnungabt170 • updated 3 months ago by laurenz.holcik0
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Tutorial: Reading csv file in minfi
... Hi, I have downloaded 450k data and want to read in minfi. When i downloaded the file it comes with csv, txt and excel files, but it does not have any idat files. I have tried to read the csv file in minfi according to the tuitorial. But i get below error. Did anybody have the same problem and kno ...
minfi tutorial infinium 450k written 3 months ago by lalchungnungabt170
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Extract gene ID
... Hi, I have microarray expression data set which was annotated with **pd.hugene.1.1.st.v1** and i want to extract the gene ID from the file. Below is the script i used and i give out many **NA** gene ID. I just want to confirm if this is the correct way of doing it. Thank you in advance! ``` > l ...
pd.hugene.1.1.st.v1 hugene11sttranscriptcluster.db written 4 months ago by lalchungnungabt170 • updated 4 months ago by James W. MacDonald50k
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Creating GRanges object
... I have a methylation data in GenomicRatioSet (i call it Mset). 1. I extracted the methylation beta values **MB_betas=getBeta(Mset)** 2. Next, i extracted the co-ordinates as you have suggested **MB_granges=granges(Mset)** 3. I wanted to assign the meta-column of the GRanges i have obtained ...
microarray minfi granges methylation genomicratio written 5 months ago by lalchungnungabt170 • updated 5 months ago by James W. MacDonald50k
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Subsetting GRanges objext
... Hi, I have a GRanges object "MB_granges" which has data from Chr1 - Chr22, also ChrX and ChrY. I had removed ChrX and ChrY using the following command.  > seqnames(MB_granges) factor-Rle of length 485512 with 24 runs Lengths: 46857 34810 25159 20464 24327 36611 30017 20950 9861 24388 ... 21 ...
granges subsetting written 10 months ago by lalchungnungabt170 • updated 10 months ago by James W. MacDonald50k
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makeTxdbFromUCSC fails to download
... Hi, The following error occur when trying to download hg19 known gene. I am using rtracklayer 1.38.3 >hg19db <- makeTxDbFromUCSC(genome = "hg19",tablename ="knownGene") Error in names(trackIds) <- sub("^ ", "", nms[nms != "new"]) : 'names' attribute [212] must be the same length as th ...
rtracklayer genomicfeatures maketxdbpackagefromucsc written 11 months ago by lalchungnungabt170 • updated 11 months ago by James W. MacDonald50k

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