Which platform is better for performing microarray data analysis? agilent, affymetrix or illumina?

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How to classify Tumor Mutation Burden into TMB high, medium and low groups ?

Tumor mutational burden (TMB) is a measure of the number of gene mutations inside the cancer cells. TMB of a tumor sample is calculated by the number of non-synonymous somatic mutations per...

01 September 2020 4,519 1 View

How to extract list of proteins delectable by immune histochemistry?

Is there any database or tool where I can retrieve list of proteins detectable by immune histochemistry (IHC)?

02 August 2020 7,539 2 View

How to remove a non-ionic surfactant (eg-tween20) from the reaction mixture?

I attempted to prepare CuS nanomaterials using microemulsion method. I used tween20 as the surfactant. But found it is very difficult to remove the surfactant from microemulsion. How can we remove...

23 June 2020 5,382 17 View

How to measure Lowest Detection Limit of a sensor material in Electrochemical sensing?

I know Differential Pulse Voltametry is using to measure LOD value. But I do not know how to measure the Lowest Detection Limit of a sensor in Electrochemical sensing. Please reply. Thanks.

09 March 2020 3,371 3 View

What is the longest deletion or insertion that can be detected in next generation sequencing data analysis?

what is the longest deletion or insertion that can be detected in next generation sequencing data analysis

26 February 2020 2,844 3 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...

12 February 2020 6,258 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?

19 December 2019 764 3 View

How to get an endorsement in arXiv (cs.CG)?

I have been struggling to get endorsement for putting preprint in arXiv. What is the best method to get endorsement in arXiv for computational geometry in computer science (cs.CG)?

29 October 2019 9,281 1 View

Can any one suggest me the way of getting Agricultural SAR images? or any database available?

Agri-SAR image database?

24 July 2018 4,776 3 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?

06 February 2018 6,620 5 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Has anyone tried to scan fluorescence IHC slides with microarray scanner?

I have an old slide microarray scanner (VIDAR Revolution 4200) and would like to give it a "second life", as IHC scanner array (fluorescence dyes), FISH over tissue or similar. Has anyone tried...

24 February 2021 9,210 1 View

Can I use FLEXBAR to detect and remove barcodes out of my short reads without demultiplexing ?

Hello, I have demultiplexed my short reads and I have removed the Illumina adapter left in the sequences and now I need to remove the barcodes used by the sequencing centre from my reads. I have...

22 February 2021 9,873 3 View

Qiime2- No reads passed the filter. How to set the trunc value?

Hi, I am working on some 16S sequencing data, and seems some of them are low quality. I am not sure how to set the trunc value in dada2. qiime dada2 denoise-paired \ --i-demultiplexed-seqs...

30 January 2021 6,213 3 View

What is your raw statistical treatment preference?

Hi, I have raw data from [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array that I want to process using the Expresso function for Affymetrix microarrays. My samples include tumor...

22 January 2021 1,527 3 View

How do I get ConsistencyDupSNP.sh file required for genotype consistency quality control step of genotyping data obtained from GSA 24 v2.0 ?

Genotyping data is from Illumina Global screening array 24 v 2.0 and ConsistencyDupSNP.sh file contains list of pair of duplicated SNPs in GSA24 v 2.0.

18 December 2020 1,966 3 View

Why is the gene expression of one sample uniformly higher than that of the other in the microarray gene expression analysis?

Hi all, Currently, I'm working on a project to analyze gene expression from RNA which is extractred two different samples by microarray. The results showed that almost all gene expression was...

12 December 2020 3,918 2 View

Is all normalization for microarray the same?

What i know, microarray data has vsn, loess and quantile normalization . i am dealing with GEO microarray datasets where i have to find the differential expresssed genes for NPC. im planning on...

10 December 2020 1,496 3 View

Is there any miRNA fluorescent labeling kit (or methods) that does not affect (add) the length of the miRNA?

I want to label my target miRNA and see the miRNA trafficking. But I don't want to use any plasmid or radioactive label. I need the fluorescent label that will not affect the length of my...

06 December 2020 8,471 3 View

Could anybody provide insights the best tools to create a custom database for taxonomy assignment of metagenomic data?

I am interested in the different tools that can be used to create custom databases for targeted sequencing and how to trim the databases based on the amplicon size? Also, should custom databases...

02 December 2020 3,105 3 View