User: dz2353

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dz235390
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Posts by dz2353

<prev • 30 results • page 1 of 3 • next >
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Comment: C: How to evaluate different RNA-seq normalization method?
... Thank you for your reply. I agree with you. There is no need to take too much time on normalization. For the assumption you mentioned, can I understand it as most of the genes between samples show similar expression levels? ...
written 12 days ago by dz235390
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How to evaluate different RNA-seq normalization method?
... Hi there, Is there any standard or strategy to evaluate the normalization method of reads count from RNA-seq data? I would like to compare the same gene expression level between different samples. I know I do not need to take care of the exon length, just normalize the sequencing depth. I choose so ...
rna-seq written 12 days ago by dz235390 • updated 10 days ago by Kevin Blighe56k
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Comment: C: How to deal with the .sra.vdbcache files after downloading a sra file?
... I emailed to NLM-support and they replied to me as below: The "vdbcache" files speed up the access to "sra" files that contain difficult or noisy data. Please note that the existence of these adjunct files does not mean that extraction to FASTQ will be fast; they are created only in cases where nee ...
written 23 days ago by dz235390
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Can I add the read counts to the re-sequenced read counts directly?
... Hi there, I have sequenced my samples twice. Can I add the first-time read counts to the second-time read counts directly? I just check the correlation and performed the PCA analysis. But I am not sure if I need to remove the batch effect? Thanks for any answer and ideas. ...
rna-seq written 26 days ago by dz235390 • updated 26 days ago by swbarnes27.5k
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How to analyze the 450K methylation data from UCSC Xena?
... Hi, there, I am working on the 450k methylation microarray data coming from the UCSC Xena. I plan to use minfi or ChMAP to detect the DMCs and DMRs, but the input files for those two packages are in .idat format. The data come from UCSC Xena is not that kind of format. Any advice and suggestions? A ...
R written 7 months ago by dz235390 • updated 7 months ago by RamRS26k
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How to identify lncRNAs from a probe set?
... Hi, there, I downloaded a microarray from the GEO database. The platform is GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]. I used a package from Bioconductor to transform the prob id to Ensembl id. After that, I downloaded the lncRNA annotation from GENCODE, ...
rna-seq written 10 months ago by dz235390
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Comment: C: Question about how to transform RSEM expected_count of TCGA TARGET GTEX to integ
... Yep, I did (2^x)-1 but the result is not an integer format cause the scale. I will round them. Thanks a lot! ...
written 10 months ago by dz235390
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Question about how to transform RSEM expected_count of TCGA TARGET GTEX to integers?
... Hi, there I downloaded RSEM expected_count data of TCGA TARGET GTEX from UCSC Xena to perform differential expressed analysis. I noticed the unit is log2(x+1), but I failed to turn the data into integers. The input of DESeq2 should be a matrix with integers. Any suggestions? Thanks in advance! Bes ...
rna-seq written 10 months ago by dz235390 • updated 10 months ago by i.sudbery7.3k
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How to deal with the .sra.vdbcache files after downloading a sra file?
... Hi, there I have downloaded some .sra files by using prefetch command from GEO database. After that, I found some cache files in the same folder. The extension is .sra.vdbcache or .sra.vdbcache.cache. So I was wondering if I could delete them or how to deal with them? Does it mean that I do not dow ...
rna-seq written 11 months ago by dz235390
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Comment: C: How to assign the result of a command to a variable in shell script?
... Thank u for your reply in detail and I make sense how does it work! ...
written 11 months ago by dz235390

Latest awards to dz2353

Popular Question 5 months ago, created a question with more than 1,000 views. For How to deal with the case that one gene symbol matches multiple ensembl ids?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Pathway analysis and Gene enrichment Analysis Queries

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