User: J. Smith

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J. Smith0
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Posts by J. Smith

<prev • 16 results • page 1 of 2 • next >
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Comment: C: May I use NB.MClust package for RNASeq genes clustering instead of samples clust
... I want to use it to cluster RNASeq count data downloaded from TCGA. Genes refers to row names of TCGA count matrix here. I mean, I want to find groups of genes having similar counts across either normal conditions or separately in tumor conditions. I have already separated data for two conditions. ...
written 26 days ago by J. Smith0
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May I use NB.MClust package for RNASeq genes clustering instead of samples clustering?
... Hi Friends, I have find this paper https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2556-9 for RNASeq data clustering (CRAN package: NB.MClust: Negative Binomial Model-Based Clustering). They have used it for samples clustering in RNASeq data. Can it be also possible to cl ...
R rna-seq nb.mclust written 26 days ago by J. Smith0 • updated 1 day ago by qian.li100000
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Comment: C: What is the accurate order of preprocessing steps in DNA Microarray gene express
... Thanks a lot for your extensive response with reference papers. ...
written 3 months ago by J. Smith0
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Comment: C: What is the accurate order of preprocessing steps in DNA Microarray gene express
... Thanks a lot for your response and referred package. ...
written 3 months ago by J. Smith0
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Comment: C: What is the accurate order of preprocessing steps in DNA Microarray gene express
... Thanks a lot. Now I have understood, there are a lot more preprocessing steps which I have to carry out before we can apply limma for differentially expressed genes. And limma can be applied with the final preprocessed data only. But can you please tell me why it is different from RNASeq? I mean why ...
written 3 months ago by J. Smith0
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What is the accurate order of preprocessing steps in DNA Microarray gene expression analysis?
... Hi friends, I have downloaded DNA Microarray data from NCBI. Data contains both control samples and affected samples for all genes. I want to perform downstream analysis like clustering, classification. I know that some preprocessing steps like normalization, log2 transformation and differential ex ...
preprocessing limma sam microarray written 3 months ago by J. Smith0 • updated 3 months ago by Santosh Anand4.9k
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Comment: C: What is the most suitable normalisation technique for RNASeq data?
... Thanks a lot again for your extensive help. Sorry for asking silly question again as I am new to this area. Whether in NCBI for all accession series home page, is there any distinct text written to mention it's RNASeq or scRNASeq? ...
written 3 months ago by J. Smith0
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Comment: C: What is the most suitable normalisation technique for RNASeq data?
... Thanks a lot friend. ...
written 3 months ago by J. Smith0
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Comment: C: What is the most suitable normalisation technique for RNASeq data?
... Thanks a lot... One more question, whether there is any difference in Differential Expression analysis techniques and Normalization procedure for single cell RNASeq (scRNASeq) data and RNASeq data? And how do I ensure whether a NCBI geo series data is just RNASeq or scRNASeq? I mean is there any dis ...
written 3 months ago by J. Smith0
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Comment: C: What is the most suitable normalisation technique for RNASeq data?
... Thanks for your response. I have read vst and rlog. Actually, I want to know whether any other better normalisation techniques available than using vst or rlog? Probably vst and rlog techniques were proposed quite a few years back. I want to know whether any recent better technique available or not. ...
written 3 months ago by J. Smith0

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Popular Question 11 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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