Showing : NCBI • reset
2
votes
3
replies
482
views
NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
Rstudio cDNA ensembldb NCBI
4 months ago R_Page • 0
2
votes
5
replies
758
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
5 months ago j_denton • 0
0
votes
0
replies
629
views
getGFFSet function CRASHES R session
getGFF NCBI biomartr biomaRt
2.7 years ago Matan G. ▴ 60
2
votes
4
replies
990
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI NCBI SQL AnnotationForge
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
1
vote
5
replies
1.3k
views
Gene Ontology analysis
ontology edger limma ncbi organism package
updated 4.1 years ago by 50k • written 4.1 years ago by ▴ 20
0
votes
4
replies
2.2k
views
Rsubread function buildindex cannot handle the GRCh38.p7 reference from NCBI
rsubread ncbi GRCh38 hg38
updated 7.5 years ago by ★ 3.6k • written 7.5 years ago by • 0
0
votes
0
replies
1.4k
views
Search SRA based on BioSample Attributes
ncbi sra search
8.3 years ago massacomgrao • 0
8
votes
7
replies
3.4k
views
Generating a proper TxDb instance from NCBI GFF Annotations File
ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb
updated 8.3 years ago by 16k • written 8.3 years ago by ▴ 10
2
votes
2
replies
3.2k
views
How to Normalize the Microarray Data Obtained from ncbi?
microarray normalization ncbi
updated 9.0 years ago by 65k • written 9.0 years ago by ▴ 20
0
votes
1
reply
1.2k
views
.getNcbiURL returns old NCBI url ?
annotate ncbi url
9.3 years ago reuma • 0
10 results • Page 1 of 1
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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