User: Maximilian

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Maximilian10
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2 years, 6 months ago
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3 years, 1 month ago
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Posts by Maximilian

<prev • 19 results • page 2 of 2 • next >
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Comment: C: Question about Agilent microarray data measurement
... Dear Mr. Picollo, thank you for your answer. I have tried your suggested way: > library(limma)​​ The file "targets.txt" contains all Agilent RAW .txt files and has this format: SampleNumber FileName Condition 1 GSM1436498_Parent_replicate1.txt NONE 2 GSM1436499_Parent_replicate2.txt NONE 3 ...
written 3.1 years ago by Maximilian10
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Comment: C: Question about Agilent microarray data measurement
... Mr. Picollo, thank you for your answer. I am sorry for my cryptic question, I will explain it again: In the Agilent RAW data I am using (from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=+GSE59408) in column 'ControlType' the respective genes on the microarrays  are assigned to different valu ...
written 3.1 years ago by Maximilian10
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Question about Agilent microarray data measurement
... Dear bioconductor forum, I need help with getting the data I want from agilent microarrays from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=+GSE59408. I used the Bioconductor package "limma" to read in the data from the single-color Agilent microarrays and then the package "SCAN.UPC" to get ...
microarray limma scan.upc agilent written 3.1 years ago by Maximilian10
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Comment: C: Question regarding Bioconductor package "affy" and custom-commercial platform
... Dear Mr. Hooiveld, I understand what you wrote. I am sorry I asked too unspecific question and didn't really understand the material. I didn't want to appear so demanding. Thank you, Mr. Hooiveld, for your useful links. I will come back with more knowledge and more specific and understandable quest ...
written 3.1 years ago by Maximilian10
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Comment: C: Question regarding Bioconductor package "affy" and custom-commercial platform
... Dear Mr. MacDonald, thank you for your response. With 'probe table' I mean Probe Set Data in Tabular Format for the respective Affymetrix .CEL files. I assumed you need a specific Probe Set Data in Tabular Forma​t for each respective type of Affymetrix microarray. For example for the commercial Af ...
written 3.1 years ago by Maximilian10
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Comment: C: Question regarding Bioconductor packages "affy" and "agilp"
... Dear Mr. Hooiveld, thank you very much for your suggestion with the package "scan.upc". I read the manual and found the sample code but because I am a beginner with Bioconductor and R in general I just want to ask you again: all I need to give in is result = UPC_TwoColor("sample_Agilent_input_fi ...
written 3.1 years ago by Maximilian10
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Comment: C: Question regarding Bioconductor packages "affy" and "agilp"
... Dear Mr. MacDonald, thank you for your response. The Agilent platform design files I am referring to are accessible on the GEO database under accession number GPL18948: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL18948 An example for the resulting RAW data is accessible on the GEO datab ...
written 3.1 years ago by Maximilian10
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Question regarding Bioconductor package "affy" and custom-commercial platform
... Dear Ladies and Gentleman, I am trying to use a custom-commercial Affymetrix platform called 'Affymetrix Escherichia coli full sequence array (EcFS) [EcFS_1, EcFS_2, and EcFS_3]'. The platform data can be found under the GEO accession number GPL13336: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi ...
affy written 3.1 years ago by Maximilian10
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Question regarding Bioconductor packages "affy" and "agilp"
... Dear Ladies and Gentlemen, I have a question regarding the two Bioconductor packages "affy" and "agilp". For my work I need to use expression data from Agilent software in a .txt file and then use this data to create tissue specific models with the help of the COBRA toolbox. To use the COBRA funct ...
affy written 3.1 years ago by Maximilian10

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For Alternative packages to limma for analysis of microarray datasets

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