User: Guido Hooiveld

gravatar for Guido Hooiveld
Guido Hooiveld2.3k
Reputation:
2,280
Status:
Trusted
Location:
Wageningen University, Wageningen, the Netherlands
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
11 years, 4 months ago
Email:
g*************@wur.nl

Posts by Guido Hooiveld

<prev • 371 results • page 2 of 38 • next >
0
votes
1
answers
146
views
1
answers
Answer: A: How to process Affymetrix HT HG-U133+ PM Array Plate
... Please familiarize yourselves a little with the design of the Affymetrix arrays. The design of the HG-U133+ PM array differs from the 'original'  HG-U133 Plus 2.0 array at two points, of which this is the relevant one: "Only perfect match (PM) probes from the cartridge design were retained, while mi ...
written 12 weeks ago by Guido Hooiveld2.3k
0
votes
3
answers
113
views
3
answers
Answer: A: hgu133plus2hsentrezgcdf or hgu133ahsentrezgcdf packages not installing
... Unfortunately biocLite() will not automagically download the custom (remapped) CDF you would like to use from the repository of the MBNI group. You rather have to download them directly by: install.packages("http://mbni.org/customcdf/22.0.0/entrezg.download/hgu133ahsentrezgcdf_22.0.0.tar.gz", type ...
written 12 weeks ago by Guido Hooiveld2.3k
0
votes
1
answers
66
views
1
answers
Answer: A: how to generate CDF and before normalisation and after normlisation plot for Cla
... No, you should not use / generate a CDF to analyze these arrays. You rather should analyze these type of arrays using the package oligo (link) in combination with the corresponding platform design package (link). In the vignette (PDF) of oligo it is explained how to create the plots you are interes ...
written 3 months ago by Guido Hooiveld2.3k
0
votes
1
answers
230
views
1
answers
Comment: C: ReactomePA - Pathway analysis for DE porcine genes
... Likely because Guangchuang did not specify any significance cutoff (he set the cutoffs for both p-value and q-value to 1, i.e. no significance filtering), and you set the p-value cutoff at 0.05 (which is apparently too strict for your experiment). ...
written 3 months ago by Guido Hooiveld2.3k
0
votes
2
answers
270
views
2
answers
Comment: C: How to normalize mouse gene 1.0st arry using frma?
... Basically the message tells you what is going on: for the current version of Bioconductor (R-3.4.x) only 3 predefined frozen RMA vectors are available for mouse arrays, i.e. mogene.1.0.st.v1frmavecs, mouse4302frmavecs, and mouse430a2frmavecs. For the arrays you mention these vectors/info isn't avail ...
written 3 months ago by Guido Hooiveld2.3k
0
votes
1
answers
176
views
1
answers
Comment: C: How to create a customized OrgDb in order to perform kegga analysis?
... Aha, AFAIK in that case you can use the argument species.KEGG = "ko" when using the function kegga(). Assuming DEGs is a character vector with the differentially expressed KO IDs, something like: k<- kegga(DEGs, species.KEGG = "ko", FDR = 0.05) ...
written 3 months ago by Guido Hooiveld2.3k
0
votes
1
answers
176
views
1
answers
Comment: C: How to create a customized OrgDb in order to perform kegga analysis?
... Let me ask you in turn: is there any pathway / annotation info publicly available for this organism? At KEGG apparently not... Being a person working with T gamsii I suppose you should know this.... If there isn't, you cannot expect members of this (Bioconductor) support site to give you a useful an ...
written 3 months ago by Guido Hooiveld2.3k
0
votes
0
answers
189
views
0
answers
Comment: C: problem using AnnotationDbi
... Based on this error:  there is no package called ‘digest’, it likely means you have to install the package digest first. source("https://bioconductor.org/biocLite.R") biocLite("digest")   ...
written 4 months ago by Guido Hooiveld2.3k
0
votes
5
answers
303
views
5
answers
Comment: C: Microarray analysis using RMA method using affy, limma
... The workflow at F1000 may also be a good place to start. ...
written 4 months ago by Guido Hooiveld2.3k
0
votes
1
answers
161
views
1
answers
Comment: C: limma package for DEGs analysis
... Please be more specific by providing the output of the function that apparently is not doing what you expect it do do, because "it is not working" is not really informative... and people don't have the time to reproduce your lines of code without having access to the raw data. In addition, please r ...
written 4 months ago by Guido Hooiveld2.3k

Latest awards to Guido Hooiveld

Popular Question 11 months ago, created a question with more than 1,000 views. For Design and contrast question limma (additive or nested or duplicateCorrelation())??
Scholar 11 months ago, created an answer that has been accepted. For A: Queries around makeOrgPackageFromNCBI
Scholar 11 months ago, created an answer that has been accepted. For A: clusterProfiler: Which GO version is used behind ?
Popular Question 11 months ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Popular Question 11 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 11 months ago, created a question with more than 1,000 views. For problem generating Chinese hamster txdb from GFF file
Popular Question 11 months ago, created a question with more than 1,000 views. For minfi, bumphunter + complex experimental design, and 3 other 450K queries
Popular Question 11 months ago, created a question with more than 1,000 views. For package/function for median center & unit variance
Popular Question 11 months ago, created a question with more than 1,000 views. For limma: one sample t-test + covariate
Popular Question 12 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Scholar 12 months ago, created an answer that has been accepted. For A: Taking surrogate variable into account before running PCA
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Taking surrogate variable into account before running PCA
Popular Question 12 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Testing for DE genes
Popular Question 16 months ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 2.2 years ago, created a question with more than 1,000 views. For import DOT (GraphViz) into Cytoscape
Popular Question 2.2 years ago, created a question with more than 1,000 views. For LIMMA: warning coercing argument of type 'double' to logical
Supporter 2.2 years ago, voted at least 25 times.
Centurion 4.1 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 291 users visited in the last hour