RNA-Seq analysis cummerbund package in R?

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What is the possibility of replicates being different from other replicates of same sample?

I have analyzed the dataset of GSE38132 from gene expression omnibus. The data is from cell line breast cancer ZR-75-1 which comprises of 9 conditions with 4 replicates for each condition making...

01 February 2020 8,505 4 View

How to perform normalization and calculate when there are multiple groups ?

I have 4 sample [control, pre-treatment, post-treatment, metastais] with 4 replicates which make total 4x4 = 16 samples I want to perform comparison of control with all other groups. For the said...

01 February 2020 5,120 2 View

How does batch correction of gene expression data affect accuracy?

I have two batches of samples which were collected during two time period. If I perform batch correction to remove batch effect will it affect the downstream analysis of gene expression studies?

11 December 2019 1,272 3 View

Does latest version of dbSNP build 151 have all 'rsids' (SNP ids)?

dbSNP has got different build (140 to 151). Does the latest version dbSNP build 151 have all snp ids (rsids) that are present in previous build

06 July 2018 4,574 0 View

Is it possible to get odds ratio of a snp from clinvar database?

Some database like ebi gwas provides odds ratio for snps. I wanted to know whether clinvar database provides the same?. I have whole data of clinvar in excel but I can not find odds ratio in it.

05 June 2018 9,591 2 View

What are the best tools for Data Mining Techniques for Harvesting Data from the Internet?

I want to extract the data from the internet with specific medical terms. Which are the available tools with best accuracy or output?

01 February 2018 9,754 7 View

Is combined approach from different research paper a novel methodology?

Consider, 4 research paper with different methodologies to prioritize genes. Combining these methods to single pipeline, can we call it as a "novel method" as together they can not be found in any...

01 February 2018 9,978 2 View

What is the present status of Next Generation sequencing in Clinical Diagnosis?

What is the present status of Next Generation sequencing in Clinical Diagnosis?. Is it well defined to make a conclusion for diagnosis?.

10 November 2017 8,687 3 View

Organs and part of organ classification?

Hi, I think there are about 80 organs in the human body. When I searched for list of all organs different sites are showing different list. Are there any books or publication that clearly mentions...

10 November 2017 950 5 View

Identifying transcript expression from Exome Sequencing?

RNA-Seq is well known for calculating transcript expression. But, researches also do variant calling on RNA-seq data. In such case all mutations can't be identified due to alternative splicing....

07 August 2017 8,057 8 View

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

Do we need to write protocol for a second study of a systematic review that has been registered and published?

I have conducted and published a systematic review and meta-analysis research with the topic related to public health and health pomotion (protocol was registed in PROSPERO). Now we want to...

03 March 2021 8,920 3 View

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 View

1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature)?

1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature-based reflection)? Thank you for your time and for...

03 March 2021 2,870 3 View

What degree of missing data in a particular case/participant results in Expectation-Maximisation no longer working?

I'm dealing with a mediation model and am using the PROCESS module in SPSS. Due to SPSS and PROCESS being limited in the imputation methods - being unable to handle multiple imputation - the other...

02 March 2021 4,362 1 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 View